{ "schema_version": "7.0", "checked": "2026-11-09", "title": "Segmentation Clock Literature & Data Explorer", "scope": "15篇文献；7组重绘，包含数值矩阵、细胞轨迹及2组视频色阶近似。数据分级与样本限制保留。", "papers": [ { "id": "chhabra-2026", "short": "Chhabra 2026", "title": "Cycles upon cycles—Temperature scaling of medaka development", "authors": [ "Sapna Chhabra", "Victoria Mochulska", "Carina B. Vibe", "Anubhuti Anushree", "Kristina S. Stapornwongkul", "Thomas Thumberger", "Joachim Wittbrodt", "Paul François", "Alexander Aulehla" ], "year": 2026, "journal": "PNAS", "doi": "10.1073/pnas.2619120123", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13663819/", "species": "Oryzias latipes", "species_label": "Oryzias latipes · 青鳉", "systems": [ "ex vivo" ], "system_description": "Her7-mVenus青鳉尾部外植体；batch1为13–15 somites，batch2为16–17 somites，培养基和成像年代不同。", "tissue": "尾部外植体，包括PSM与tailbud。", "conditions": "恒温22/27/32°C；21–27°C温度循环12h/24h（batch1）及6h（batch2，对应27°C对照）。跨批次速度比较使用作者校正。", "origin": "live", "origin_label": "活体时序成像 · ex vivo", "reporter_short": "Her7–mVenus", "reporter_tags": [ "Her7", "mVenus" ], "reporter_construct": "内源her7位点CRISPR knock-in Her7-mVenus融合报告；不是promoter-only转录reporter。", "reported_target": "Her7蛋白的荧光动态；phase由强度经过wavelet或Hilbert推算。", "patterns": [ "振荡传播波", "相位梯度", "温度缩放", "形态学 somite boundaries" ], "figure_focus": "Fig2C：22/27/32°C强度kymograph；2E：相同数据按振荡周期重标时间。Fig3：phase SVD分解/重建。Fig5A/B：循环温度实验；5E/F：模拟。", "time_axis": "Fig2C横轴0–12 h；2E横轴0–6 cycles。样本TIFF列为时间，27°C样本间隔10 min；绝对起点和裁剪窗口需保留。", "space_axis": "Fig2C/E纵轴Space (µm)，0在上、位置向下增加；样本TIFF行为空间。batch1恒温为center-of-mass registration，不能套用anterior注册原点。", "time_resolution": "Methods：10 min/frame；32°C恒温5 min/frame。所读20200815 P1的data_settings也为10 min。TIFF finterval=1及XResolution不作为物理时间标定。", "space_resolution": "成像512×512，1.38µm/px；5–10个z平面、间隔7µm；20×/NA0.8。所读27°C样本data_settings dx=1.38µm。", "replicates": "本次解码1个27°C生物样本的强度/相位配对。论文Fig5按条件报告重复；未把文件个数或配对两个文件计为生物学n。", "calibration_short": "10 min · 1.38 µm/px（27°C）", "preprocessing": "最大z投影、Gaussian σ4。第一种配准：FIJI rigid-body center-of-mass，20px宽折线取样；另一种：Ilastik mask→Matlab skeleton→midline横向平均及anterior注册。batch1 wavelet；batch2正文采用Hilbert。SVD作用于phase，不直接作用于原始强度。", "summary": "温度改变分节时钟速度，空间相位梯度相对稳定。已有公开强度/相位kymograph与代码，适合对照poster的波形、相位梯度和尺度关系。", "priority": 0, "recommendation": "优先用已核27°C样本重画实验I(t,p)，再比较phase gradient与周期；随后分批次扩展温度条件。不要直接把实验荧光或相位当作模型基因浓度。", "availability_status": "verified_content", "availability_summary": "已读1对处理后的数值kymograph；原始栈未定位。", "availability_filters": [ "论文图已核实", "数值矩阵已读取", "原始栈未定位" ], "verification_scope": "正式版全文、Fig2原图、Fig3/5图注、bioRxiv/Crossref身份、GitHub完整树、MIT和说明文件；固定commit下载并解码一对27°C强度/相位TIFF。未复现SVD或核验所有样本。", "missing": [ "原始Her7-mVenus成像栈", "每个其他样本的轴、掩码、有效区域及批次核验", "已下载样本与Fig2代表面板的确切对应尚未确认" ], "caveats": [ "处理后的2D数值TIFF不是原始成像栈。", "27°C样本是center-of-mass注册；不能标作anterior注册。", "TIFF内置时间/分辨率字段与实际生物时间标定不同；使用Methods+data_settings的10min与1.38µm。", "两批样本培养基、发育阶段、配准与相位提取不同；跨条件比较需保留这些差异。", "仓库README对24h批次及6h目录名有不一致，须与正文和实际目录一起核对。", "相位矩阵是同一荧光数据的派生结果；不是独立样本，也不是绝对浓度。" ], "sources": [ { "id": "C1", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13663819/", "location": "Published article / Methods / Data availability", "note": "PNAS正式版全文已读；Her7-mVenus、ex vivo尾部外植体、成像与配准方法、批次差异和GitHub入口。" }, { "id": "C2", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13663819/#fig02", "location": "Figure 2 C/E 图注与原图", "note": "C为22/27/32°C实验强度kymograph（横轴hours、纵轴µm向下）；E为相同图按振荡cycles重标时间。已视觉核对坐标。" }, { "id": "C3", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13663819/#fig03", "location": "Figure 3 A–C", "note": "从强度推算phase，再做SVD；重建/拟合不等于独立实验原图。" }, { "id": "C4", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13663819/#fig05", "location": "Figure 5 A/B/E/F", "note": "A/B为温度循环实验分析；E/F为alpha模型模拟。" }, { "id": "C5", "url": "https://github.com/victoria-mochulska/cycles_upon_cycles/tree/c8942dd1aeeea790e2cb141662b9ef235756d2c4", "location": "Pinned repository tree and LICENSE", "note": "公开仓库、完整文件树、MIT许可证已读；含处理后的强度/相位TIFF和分析代码，不等同原始成像栈。" }, { "id": "C6", "url": "https://github.com/victoria-mochulska/cycles_upon_cycles/blob/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs/Read%20me", "location": "Data Read me", "note": "27°C batch1为center-of-mass registration。24h批次说明与正文、6h目录命名与实际目录有差异，后续跨条件处理须核对。" }, { "id": "C7", "url": "https://github.com/victoria-mochulska/cycles_upon_cycles/blob/c8942dd1aeeea790e2cb141662b9ef235756d2c4/SVD_analysis/src/data_settings.py", "location": "sample_names / sample_dt / sample_dx", "note": "20200815 P1归于TE_27C_14ss；dt=10 min、dx=1.38µm。仅读取代码，未执行仓库软件。" }, { "id": "C8", "url": "https://raw.githubusercontent.com/victoria-mochulska/cycles_upon_cycles/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs/batch1_chronic_27C/intensityKymo/Kymo_20200815_P1.tif", "location": "Kymo_20200815_P1.tif numeric readback", "note": "已完整解码279×119 uint16；33,201个有限值，范围6561–33060；已核SHA256及Git blob。" }, { "id": "C9", "url": "https://raw.githubusercontent.com/victoria-mochulska/cycles_upon_cycles/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs/batch1_chronic_27C/phaseKymo/phase_Kymo_20200815_P1.tif", "location": "phase_Kymo_20200815_P1.tif numeric readback", "note": "同尺寸float32相位，33,201个有限值，约−π至π；同一样本的派生量，非独立重复。" }, { "id": "C10", "url": "https://api.biorxiv.org/details/biorxiv/10.64898/2026.04.29.721546", "location": "bioRxiv API DOI record", "note": "用户原链接v1发布于2026-05-02；published字段关联PNAS DOI。保留预印本身份，文献库采用正式版。" }, { "id": "C11", "url": "https://api.crossref.org/works/10.1073/pnas.2619120123", "location": "Publisher-deposited metadata", "note": "2026-10-08，PNAS 123(41)，e2619120123；正式版CC BY 4.0；Paul François共同作者。" }, { "id": "C12", "url": "https://github.com/victoria-mochulska/cycles_upon_cycles/tree/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs/batch1_chronic_27C", "location": "Local numerical re-render / render_kymograph.py", "note": "强度与phase已按原矩阵重绘；完整方法、源文件SHA256、色标与轴边界见figures/chhabra-2026/render-provenance.json。未额外平滑、裁剪、归一化或重算phase；未加低信号质量掩码。" } ], "field_evidence": { "species": [ "C1" ], "system_description": [ "C1" ], "tissue": [ "C1" ], "conditions": [ "C1" ], "reporter_construct": [ "C1" ], "reported_target": [ "C1" ], "preprocessing": [ "C1" ], "replicates": [ "C1" ], "time_axis": [ "C2", "C3", "C4" ], "space_axis": [ "C2", "C3", "C4" ], "figure_focus": [ "C2", "C3", "C4" ], "kymograph": [ "C2", "C3", "C4", "C12" ], "time_resolution": [ "C1", "C6", "C7", "C8", "C9" ], "space_resolution": [ "C1", "C6", "C7", "C8", "C9" ] }, "assets": [ { "level": "figure", "level_label": "论文图", "label": "Fig. 2C/E · 温度与时间缩放", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13663819/#fig02", "format": "HTML / WebP", "bytes": null, "status": "verified_content", "evidence": "已读图注并视觉核对完整原图。C以小时、E以cycles表示同组实验；均为强度kymograph。", "license": "CC BY 4.0", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "数值 kymograph", "label": "强度 · 27°C / 20200815 P1", "url": "https://raw.githubusercontent.com/victoria-mochulska/cycles_upon_cycles/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs/batch1_chronic_27C/intensityKymo/Kymo_20200815_P1.tif", "format": "TIFF · uint16 · 279 × 119", "bytes": 68273, "status": "verified_content", "evidence": "完整下载并解码；空间行×时间列=279×119，全部有限值。uint16范围6561–33060。 10 min、1.38µm依据Methods及data_settings；TIFF自身时间/分辨率标签不能直接作为物理轴。仅核对这一对样本，未认定为Fig2代表样本。", "license": "仓库根目录 MIT LICENSE（Victoria Mochulska, 2026）；见随附许可证。", "checked": "2026-11-09", "local_path": "data/samples/chhabra-2026/Kymo_20200815_P1.tif" }, { "level": "matrix", "level_label": "数值 kymograph", "label": "相位 · 27°C / 20200815 P1", "url": "https://raw.githubusercontent.com/victoria-mochulska/cycles_upon_cycles/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs/batch1_chronic_27C/phaseKymo/phase_Kymo_20200815_P1.tif", "format": "TIFF · float32 · 279 × 119", "bytes": 133072, "status": "verified_content", "evidence": "完整下载并解码；空间行×时间列=279×119，全部有限值。float32约−π至π。 10 min、1.38µm依据Methods及data_settings；TIFF自身时间/分辨率标签不能直接作为物理轴。仅核对这一对样本，未认定为Fig2代表样本。", "license": "仓库根目录 MIT LICENSE（Victoria Mochulska, 2026）；见随附许可证。", "checked": "2026-11-09", "local_path": "data/samples/chhabra-2026/phase_Kymo_20200815_P1.tif" }, { "level": "matrix", "level_label": "数据目录", "label": "全部条件 · intensity / phase kymographs", "url": "https://github.com/victoria-mochulska/cycles_upon_cycles/tree/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs", "format": "TIFF directories", "bytes": null, "status": "listed", "evidence": "完整GitHub树已读；其他TIFF未逐文件解码。恒温与温度循环、batch1/2和配准方式应分开。", "license": "仓库根目录 MIT LICENSE；未发现单独数据许可证。", "checked": "2026-11-09" }, { "level": "code", "level_label": "分析代码", "label": "SVD / phase extraction / registration", "url": "https://github.com/victoria-mochulska/cycles_upon_cycles/tree/c8942dd1aeeea790e2cb141662b9ef235756d2c4", "format": "Python / Matlab / Groovy / notebooks", "bytes": null, "status": "listed", "evidence": "已读目录、README和data_settings.py；未安装或执行外部代码，不能称为已复现。", "license": "MIT", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "原始 Her7-mVenus z-stacks", "url": null, "format": null, "bytes": null, "status": "unknown", "evidence": "论文明确公开kymographs和codes；所读完整仓库树未定位原始成像栈。处理后的TIFF不是raw movie。", "license": "未知", "checked": "2026-11-09" } ], "media": [ { "label": "Figure 2 · 恒温实验与周期缩放", "url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce81/13663819/ca372f7edc21/pnas.2619120123fig02.webp", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13663819/#fig02", "description": "C为实验强度kymograph，E为同一组数据以cycles重标时间。完整图保留A–F。", "attribution": "Chhabra et al. · PNAS 123(41), e2619120123 (2026) · DOI 10.1073/pnas.2619120123 · CC BY 4.0. 原图未修改。", "status": "图注及原图已核实。" } ], "checked": "2026-11-09", "related_identifiers": { "preprint_doi": "10.64898/2026.04.29.721546", "preprint_v1": "https://www.biorxiv.org/content/10.64898/2026.04.29.721546v1.full.pdf" }, "kymograph": { "kind": "experimental", "short": "Kymograph · Fig. 2C/E", "selector": "原图 / 数值重绘", "order": 2, "preview": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce81/13663819/ca372f7edc21/pnas.2619120123fig02.webp", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13663819/#fig02", "panel": "Fig. 2C/E · 温度与分节波形", "panel_note": "C：实验强度图（小时）。E：同一数据按振荡周期重标时间。", "attribution": "Chhabra et al. · PNAS 123(41), e2619120123 (2026) · DOI 10.1073/pnas.2619120123 · CC BY 4.0. 原图未修改。", "focus": "时间改变，空间如何保持？", "takeaway": "从22°C到32°C，对照传播波与空间相位结构；已有数值kymograph可用。", "reporter": "Her7–mVenus · 青鳉", "time": "横轴 · C：h；E：cycles", "space": "纵轴 · µm；位置向下增加", "signal": "Her7–mVenus 荧光强度", "metrics": [ "周期", "相位梯度", "温度鲁棒性" ], "limit": "已读27°C强度/相位各1个TIFF；属处理后数据，原始栈未定位。", "model_note": "先以匹配的空间方向和时间窗口比较I(t,p)与模型观测量，再比较phase gradient。Fig3的SVD可作为低维表型思路，但论文结论不是对你的生成模型的验证。", "dataset_url": "https://github.com/victoria-mochulska/cycles_upon_cycles/tree/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs", "rendered": { "intensity": { "source_url": "https://github.com/victoria-mochulska/cycles_upon_cycles/tree/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs/batch1_chronic_27C", "attribution": "数据：Chhabra et al. · PNAS (2026) · 仓库 MIT 许可。Clock Explorer 从数值矩阵重绘；非原论文面板。", "focus": "从数据重画，和模型对照", "takeaway": "同一27°C样本，统一版式与坐标；完整保留已存数据范围。", "time": "横轴 · h；首个存储帧为 0", "space": "纵轴 · µm；首行起向下增加", "model_note": "使用公开处理后TIFF，按10min/列、1.38µm/行标定。坐标原点来自首个存储帧和行，不对应发育起点或已确认解剖位置。center-of-mass注册不等于anterior注册。重绘未额外归一化、平滑、裁剪或重算相位；nearest显示不增加信息。比较模型时需先匹配观测量、坐标方向和有效组织区。", "panel_note": "20200815 P1 · 27°C · 279×119 · 未额外平滑或裁剪", "preview": "figures/chhabra-2026/her7-27C-intensity.svg", "panel": "27°C · Her7 强度重绘", "signal": "完整强度范围 · 6,561–33,060 a.u.", "limit": "处理后矩阵；原始栈未定位。此样本与论文Fig. 2代表样本的对应未确认。", "downloads": { "svg": "figures/chhabra-2026/her7-27C-intensity.svg", "pdf": "figures/chhabra-2026/her7-27C-intensity.pdf", "png": "figures/chhabra-2026/her7-27C-intensity.png" } }, "phase": { "source_url": "https://github.com/victoria-mochulska/cycles_upon_cycles/tree/c8942dd1aeeea790e2cb141662b9ef235756d2c4/2026_PNAS_CyclesUponCycles_intensityPhaseKymographs/batch1_chronic_27C", "attribution": "数据：Chhabra et al. · PNAS (2026) · 仓库 MIT 许可。Clock Explorer 从数值矩阵重绘；非原论文面板。", "focus": "从数据重画，和模型对照", "takeaway": "同一27°C样本，统一版式与坐标；完整保留已存数据范围。", "time": "横轴 · h；首个存储帧为 0", "space": "纵轴 · µm；首行起向下增加", "model_note": "使用公开处理后TIFF，按10min/列、1.38µm/行标定。坐标原点来自首个存储帧和行，不对应发育起点或已确认解剖位置。center-of-mass注册不等于anterior注册。重绘未额外归一化、平滑、裁剪或重算相位；nearest显示不增加信息。比较模型时需先匹配观测量、坐标方向和有效组织区。", "panel_note": "20200815 P1 · 27°C · 279×119 · 未额外平滑或裁剪", "preview": "figures/chhabra-2026/her7-27C-phase.svg", "panel": "27°C · 派生相位重绘", "signal": "Wavelet 派生相位 · −π 至 π", "limit": "未加质量掩码；低信号区域的相位不能直接作生物学解释。", "downloads": { "svg": "figures/chhabra-2026/her7-27C-phase.svg", "pdf": "figures/chhabra-2026/her7-27C-phase.pdf", "png": "figures/chhabra-2026/her7-27C-phase.png" } } }, "comparison": { "id": "chhabra-2026", "short": "Chhabra 2026", "reporter": "Her7–mVenus", "kind": "matrix", "label": "Processed matrix", "source_url": "https://github.com/victoria-mochulska/cycles_upon_cycles", "origin": "First stored row", "origin_short": "存储位置", "sample": "27°C · 20200815 P1", "position_unit": "µm", "input": "data/samples/chhabra-2026/Kymo_20200815_P1.tif", "input_sha256": "5d615be397563026e89acf6c030eef61980256ba5686a41a52633bfd4108ea1b", "shape_space_time": [ 279, 119 ], "time_range_h": [ 0.0, 19.666666666666668 ], "spatial_range": [ 0.0, 383.64 ], "missing_values": 0, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 6561.0, "max": 33060.0 }, "spatial_range_um": [ 0.0, 383.64 ], "common_preview": "figures/comparison/chhabra-2026-common.svg", "full_preview": "figures/comparison/chhabra-2026-full.svg" }, "card_context": { "condition": "27°C", "sample": "20200815 P1", "source_url": "https://github.com/victoria-mochulska/cycles_upon_cycles/blob/c8942dd1aeeea790e2cb141662b9ef235756d2c4/SVD_analysis/src/data_settings.py", "evidence": "Selected batch1_chronic_27C sample; temperature and sample identity verified in archived validation.json." } } }, { "id": "lauschke-2013", "short": "Lauschke 2013", "title": "Scaling of embryonic patterning based on phase-gradient encoding", "authors": [ "Volker M. Lauschke", "Charisios D. Tsiairis", "Paul François", "Alexander Aulehla" ], "year": 2013, "journal": "Nature", "doi": "10.1038/nature11804", "url": "https://www.nature.com/articles/nature11804", "species": "Mus musculus", "species_label": "Mouse · 小鼠", "systems": [ "ex vivo", "embryo culture" ], "system_description": "E10.5 mouse tailbud-derived quasi-monolayer PSM (mPSM)；对照为含PSM的posterior embryo fragment培养成像（文中称in vivo）。", "tissue": "尾芽 mesoderm / presomitic mesoderm", "conditions": "Fibronectin基底，37°C、5% CO₂；温度对照33°C。mPSM先铺展，约20h后进入明显分节期。", "origin": "live", "origin_label": "真实 time-lapse", "reporter_short": "LuVeLu · Mesp2-GFP", "reporter_tags": [ "LuVeLu", "Mesp2-GFP" ], "reporter_construct": "LuVeLu：Lfng调控的destabilized Venus荧光reporter（原构建Aulehla2008）；另有Mesp2-GFP targeted allele。", "reported_target": "LuVeLu → Lfng / Notch相关转录活性；Mesp2-GFP → 分节分化标记。均不等于未经reporter动力学变换的基因表达浓度。", "patterns": [ "振荡传播波", "振荡停止", "固定表达条纹", "形态学 somite boundaries" ], "figure_focus": "Fig4a：用户poster所用实验kymograph及投影分析；4b实验相位梯度汇总；4c/d数值模拟。Fig1c：胚胎PSM实验kymograph；Fig1f：ex vivo mPSM实验kymograph，对应Video2。Fig3a是segment width–mPSM length散点图，不是kymograph。Fig4a/b实验，4c/d模拟；Fig3d示意。", "time_axis": "Fig1c/f：横轴Time (h)；不是视频播放秒数。", "space_axis": "Fig1c/f：纵轴Space (µm)。c为posterior→anterior，f为centre→periphery（对应mPSM后→前）。", "time_resolution": "10 min / z-stack。", "space_resolution": "原采集12-bit、512×512、1.38 µm/pixel；z-step6–8 µm；胚胎6–8层，ex vivo3–4层。", "replicates": "Fig1g周期：embryo n=12、ex vivo n=16；Fig3a：26 segments / 5 samples；Fig3b：42 waves / 7 samples。各n对应不同分析。", "calibration_short": "10 min · 视频标尺已核", "preprocessing": "Z最大强度投影；Gaussian σ=7px平滑后沿中心→边缘取线，再平滑并保存text image；去趋势、moving average、逐空间点Hilbert提相位。MOV为已渲染补充视频，未证明保留原始12-bit强度。", "summary": "Poster所引实验体系：LuVeLu同心传播波与segment scaling；Fig1f可作为实验kymograph基准，Video2文件入口已实测可达。", "priority": 3, "recommendation": "先用Fig1f/Video2复核波向、周期和随位置减速，再比较模拟；定量强度拟合仍需原始栈或text-image矩阵。", "availability_status": "verified_content", "availability_summary": "官方视频已解码 · 已提取探索性ROI矩阵；原始成像栈未定位。", "availability_filters": [ "论文图已核实", "文件响应已验证", "视频已解码", "本地提取矩阵" ], "verification_scope": "原文与图注、公开方法索引已核；Video2/5仅Range GET前1024bytes，确认HTTP206、QuickTime moov结构及总大小，未全文件下载或解码。 本轮完整解码官方视频，读取烧录时间与标尺，保存平移校正后ROI矩阵及三时点取线核查图。", "missing": [ "Video2/5完整解码及每帧时间/空间标定复核", "原始12-bit z-stack", "作者保存的text-image kymograph / intensity matrix", "原始数据及图像再利用许可" ], "caveats": [ "Fig1f是真实实验；Fig4c为phase model模拟，不能混入实验数据。", "Fig3a仅支持segment-size scaling，不是时空荧光图。", "mPSM铺展、后续收缩和取线位置改变会影响空间坐标；相位波速不是细胞运动速度。", "视频可达不等于原始成像公开；MOV压缩、强度显示映射、bit depth仍待核实。", "2013是期刊卷期年份；online publication为2012-12-19。", "新增本地重绘来自压缩视频；仅平移校正，不是组织形变/细胞追踪。不同reporter绝对亮度不可比较。" ], "sources": [ { "id": "L1", "url": "https://www.nature.com/articles/nature11804", "location": "Title / Author information / About this article", "note": "作者、DOI、2013卷期；在线发表2012-12-19。", "checked": "2026-11-09" }, { "id": "L2", "url": "https://www.nature.com/articles/nature11804/figures/1", "location": "Figure1 caption + publisher full image", "note": "c/f为真实实验kymograph；caption明确取线与传播方向，Fig1g重复数。父代理浏览器已打开图页及1417×1629原图。", "checked": "2026-11-09" }, { "id": "L3", "url": "https://www.mcgill.ca/francois-group/files/francois-group/nature_2013_lauschke.pdf", "location": "Methods: Two-photon microscopy; Image processing（文末）", "note": "公开检索缓存可读完整methods：10min、12-bit512²、1.38µm/px、z6–8µm及处理；作者站当前直接GET404，不能标PDF可下载。", "checked": "2026-11-09" }, { "id": "L4", "url": "https://www.nature.com/articles/nature11804/figures/3", "location": "Figure3 caption", "note": "3a:26segments/5samples；3b:42waves/7samples；3d是scheme。", "checked": "2026-11-09" }, { "id": "L5", "url": "https://www.nature.com/articles/nature11804/figures/4", "location": "Figure4 caption", "note": "4a/b实验测量；4c/d数值模拟。", "checked": "2026-11-09" }, { "id": "L6", "url": "https://www.nature.com/articles/nature11804#Sec12", "location": "Supplementary information: Videos1–7", "note": "公开HTML已取到；Video2对应Fig1d/f；Video5是分节期LuVeLu，Video4–7同一样本不同通道。", "checked": "2026-11-09" }, { "id": "L7", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM293_ESM.mov", "location": "2026-11-09 Range GET bytes=0-1023", "note": "HTTP206；Content-Range bytes0-1023/16373596；first atom moov，未完整下载或解码。", "checked": "2026-11-09" }, { "id": "L8", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM296_ESM.mov", "location": "2026-11-09 Range GET bytes=0-1023", "note": "HTTP206；Content-Range bytes0-1023/11245648；first atom moov，未完整下载或解码。", "checked": "2026-11-09" }, { "id": "K1", "url": "https://www.nature.com/articles/nature11804/figures/4", "location": "Figure4a–d公开图注及原图，Chrome视觉核查", "note": "a为实验时空图，带早期截断phase-wave velocity与projected mPSM length散点；c/d为模拟。a坐标0–40h、0–600µm，与用户poster截图对应。", "access": "公开图注和图片已核" }, { "id": "R1", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM296_ESM.mov", "location": "Official movie full decode and local ROI extraction", "note": "完整读取并解码。矩阵[311, 61]；t=[0.0, 10.0]h。取样/配准/标尺/hash见data/derived/lauschke-2013/extraction-provenance.json。8bit显示值不是raw荧光。" } ], "field_evidence": { "species": [ "L1", "L3" ], "system_description": [ "L2", "L3" ], "tissue": [ "L2", "L3" ], "conditions": [ "L3", "L4" ], "reporter_construct": [ "L3", "L6" ], "reported_target": [ "L3", "L6" ], "figure_focus": [ "L2", "L4", "L5" ], "time_axis": [ "L2" ], "space_axis": [ "L2" ], "time_resolution": [ "L3" ], "space_resolution": [ "L3" ], "replicates": [ "L2", "L4" ], "preprocessing": [ "L3", "L6" ], "kymograph": [ "K1", "R1" ] }, "assets": [ { "level": "figure", "level_label": "论文图", "label": "Figure1 · c/f为实验kymograph", "url": "https://www.nature.com/articles/nature11804/figures/1", "format": "JPEG / HTML", "bytes": null, "size": null, "status": "verified_content", "evidence": "父代理浏览器核实完整图1417×1629；本代理缩略图Range GET返回JPEG签名。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Supplementary Video2 · Fig1f来源", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM293_ESM.mov", "format": "MOV", "bytes": 16373596, "size": "16,373,596 bytes（约15.61 MiB）；页面15,989 kb", "status": "verified_content", "evidence": "完整下载并解码MOV；Video2共160帧，Video5共61帧。Video2画面时间增量约0.21h与名义10min不同，当前重绘选时间核实的Video5。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Supplementary Video5 · 分节期LuVeLu", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM296_ESM.mov", "format": "MOV", "bytes": 11245648, "size": "11,245,648 bytes（约10.72 MiB）；页面10,982 kb", "status": "verified_content", "evidence": "完整下载并解码MOV；Video2共160帧，Video5共61帧。Video2画面时间增量约0.21h与名义10min不同，当前重绘选时间核实的Video5。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Supplementary Video1 · embryo PSM", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM292_ESM.mov", "format": "MOV", "bytes": null, "size": "19,833 kb（页面标注）", "status": "listed", "evidence": "出版社列出；文件本体未探测。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Supplementary Video4 · brightfield边界", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM295_ESM.mov", "format": "MOV", "bytes": null, "size": "14,195 kb（页面标注）", "status": "listed", "evidence": "出版社列出；与Videos5–7同一样本，观察形态边界。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Supplementary Video6 · Mesp2-GFP", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM297_ESM.mov", "format": "MOV", "bytes": null, "size": "14,331 kb（页面标注）", "status": "listed", "evidence": "出版社列出；Mesp2-GFP最大投影。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Supplementary Video7 · 合并通道", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM298_ESM.mov", "format": "MOV", "bytes": null, "size": "19,560 kb（页面标注）", "status": "listed", "evidence": "出版社列出；GFP/YFP/brightfield overlay，brightfield线性调亮度/对比度。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "supplement", "level_label": "补充材料", "label": "Supplementary Figures1–8 / model derivation", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM291_ESM.pdf", "format": "PDF", "bytes": null, "size": "7,915 kb（页面标注）", "status": "listed", "evidence": "PDF附件已定位；包含实验补图与数学模型，未作为原始数据。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "强度 / kymograph 矩阵", "label": "作者text-image kymograph矩阵", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "evidence": "Methods明确保存过text image；所查原文/补充目录/标题与DOI检索未定位独立公开数值文件。", "license": "未知", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "原始12-bit time-lapse / z-stack", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "evidence": "未定位可验证原始成像仓库；补充MOV不等同原始栈。", "license": "未知", "checked": "2026-11-09" }, { "level": "contact", "level_label": "需要联系作者", "label": "后续可询问矩阵与原始栈", "url": "https://www.nature.com/articles/nature11804", "format": null, "bytes": null, "size": null, "status": "unknown", "evidence": "文末提供correspondence/materials联系方式；没有核实到明确原始数据分享承诺，本次未联系。", "license": "© 2013 Macmillan Publishers Limited / Nature；未核实开放再利用许可（不是 CC）。", "checked": "2026-11-09" }, { "level": "figure", "level_label": "论文图", "label": "Figure4a：poster对应实验kymograph（完整图含c/d模拟）", "url": "https://www.nature.com/articles/nature11804/figures/4", "format": "HTML / JPEG", "status": "verified_article", "bytes": null, "evidence": "实际Chrome核对公开图注：a/b为实验，c/d为模型；原图src已读取。", "license": "Nature版权；未声明CC，远程原来源预览。", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "本地视频提取矩阵", "label": "探索性 ROI 强度矩阵 · video5", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM296_ESM.mov", "local_path": "data/derived/lauschke-2013/video5-intensity.csv", "format": "CSV / NPZ · space × time", "bytes": 168617, "status": "verified_content", "source_is_input": true, "evidence": "本次从完整视频解码后提取；源视频、hash、逐帧平移、ROI和坐标数组均有记录。它不是作者公开的原始强度矩阵。", "license": "Nature copyright; no open derivative license verified.", "checked": "2026-11-09" } ], "media": [ { "label": "Figure 4a · 与poster同图", "url": "https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_Article_BFnature11804_Fig4_HTML.jpg", "source_url": "https://www.nature.com/articles/nature11804/figures/4", "description": "左上 a 与 poster 对应。a/b：实验；c/d：模拟。完整原图保留。", "attribution": "Lauschke et al. · Nature 493, 101–105 (2013), Fig. 4 · DOI 10.1038/nature11804 · © Nature / Springer Nature. 原来源加载。", "status": "实际Chrome公开figure页核对图注及原图src；a/b实验，c/d数值模拟。" }, { "label": "Figure1 · 实验kymograph c/f", "url": "https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_Article_BFnature11804_Fig1_HTML.jpg", "source_url": "https://www.nature.com/articles/nature11804/figures/1", "description": "完整原图：c为embryo PSM、f为ex vivo mPSM真实time-lapse kymograph；a为实验示意，g为周期统计。", "attribution": "Lauschke, Tsiairis, François & Aulehla. Nature 493,101–105 (2013), Fig1. DOI:10.1038/nature11804. ©2013 Macmillan Publishers Limited. 非CC；远程原图链接。", "status": "父代理实际浏览器已打开：1417×1629 px；本代理thumbnail JPEG响应头已核。" } ], "checked": "2026-11-09", "kymograph": { "kind": "experimental", "short": "Kymograph · 原图 / 视频重绘", "selector": "原图 / 视频重绘", "order": 1, "preview": "https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_Article_BFnature11804_Fig4_HTML.jpg", "source_url": "https://www.nature.com/articles/nature11804/figures/4", "panel": "Fig. 4a · Poster 中的实验时空图", "panel_note": "左上 a 与 poster 对应。a/b：实验；c/d：模拟。完整原图保留。", "attribution": "Lauschke et al. · Nature 493, 101–105 (2013) · DOI 10.1038/nature11804 · © Nature / Springer Nature. 原来源加载。", "focus": "相位梯度与组织尺度", "takeaway": "与 poster 中的时空图及波速插图一致。a 展示实验波形及截断相位梯度的外推。", "reporter": "LuVeLu · 小鼠", "time": "横轴 t · h（a：0–40）", "space": "纵轴位置 · µm（a：0–600）", "signal": "a：实验强度；c：模拟 cos(phase)", "metrics": [ "波速", "相位梯度", "长度缩放" ], "limit": "红点与虚线包含空间外推；并非所有标记位置都是直接观测。c/d 为模拟。", "model_note": "用a对照实验的波速、相位梯度和长度变化。c是该论文的模型结果，不是你的GFlowNet模型；停止相位只是该模型的pattern proxy，不能直接等同于实测体节边界。", "related_figure_url": "https://www.nature.com/articles/nature11804/figures/1", "comparison": { "id": "lauschke-2013", "short": "Lauschke 2013", "reporter": "LuVeLu", "kind": "video", "label": "Video-derived ROI", "source_url": "https://www.nature.com/articles/nature11804", "origin": "ROI start → periphery", "origin_short": "ROI 起点 → 外缘", "sample": "video5", "position_unit": "µm", "roi": "figures/lauschke-2013/video5-roi.jpg", "input": "data/derived/lauschke-2013/video5-kymograph.npz", "input_sha256": "4f391cbfb61f381f7ed132c198682e22acb77e7a92e8cdc1f25ff112b3c16cfd", "shape_space_time": [ 311, 61 ], "time_range_h": [ 0.0, 10.0 ], "spatial_range": [ 0.0, 295.23809523809524 ], "missing_values": 0, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 2.2950307903848715, "max": 223.6760683215834 }, "spatial_range_um": [ 0.0, 295.23809523809524 ], "common_preview": "figures/comparison/lauschke-2013-common.svg", "full_preview": "figures/comparison/lauschke-2013-full.svg" }, "rendered": { "intensity": { "preview": "figures/lauschke-2013/video-intensity.svg", "source_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fnature11804/MediaObjects/41586_2013_BFnature11804_MOESM296_ESM.mov", "panel": "Video 5 · LuVeLu 视频提取", "panel_note": "311×61 · 平移校正 · 宽线平均", "attribution": "Lauschke 2013 · 官方补充视频。Clock Explorer 独立取样重绘；不是原论文面板或原始荧光矩阵。", "focus": "从视频恢复时空波形", "takeaway": "去除字幕区域，以平移校正后的 ROI 逐帧取样。完整取样路径可核查。", "reporter": "LuVeLu · 小鼠", "time": "横轴 · h；10 min / 帧", "space": "纵轴 · 距 ROI 起点 µm（近似）", "signal": "8-bit 视频显示值 · 非原始荧光计数", "limit": "压缩视频 + 平移校正；未校正组织形变。用于定性波形比较，不能据此比较绝对幅值。", "model_note": "源视频已完整解码。Lauschke使用匹配明场Video4估计平移；Sonnen使用自身灰度纹理估计平移。沿预先记录的直线ROI做双线性取样和横向均值；不做时间平滑、去趋势或phase推断。空间尺度从100µm视频标尺测量，不能套原相机像素尺度。此ROI不宣称复制原论文取线；位置不是共同解剖坐标。", "downloads": { "svg": "figures/lauschke-2013/video-intensity.svg", "pdf": "figures/lauschke-2013/video-intensity.pdf", "png": "figures/lauschke-2013/video-intensity.png" }, "roi_preview": "figures/lauschke-2013/video5-roi.jpg", "metrics": [ "传播方向", "波形", "组织漂移" ] } }, "card_context": { "condition": "离体 mPSM", "sample": "Video 5", "source_url": "https://www.nature.com/articles/nature11804#Sec12", "evidence": "Official Supplementary Video 5 caption identifies the ex vivo tailbud-derived culture and LuVeLu channel. A temperature for this particular movie has not been independently verified." } } }, { "id": "sonnen-2018", "title": "Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation", "authors": [ "Katharina F. Sonnen", "Volker M. Lauschke", "Julia Uraji", "Henning J. Falk", "Yvonne Petersen", "Maja C. Funk", "Mathias Beaupeux", "Paul François", "Christoph A. Merten", "Alexander Aulehla" ], "year": 2018, "journal": "Cell", "doi": "10.1016/j.cell.2018.01.026", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/", "species": "Mus musculus", "tissue": "E10.5 posterior presomitic mesoderm (PSM); explant-derived quasi-monolayer mPSM", "conditions": "基础 mPSM 培养；另有 PDMS microfluidic chip：37°C、5% CO₂、60 µL/h；DAPT 2 µM / CHIR99021 5 µM pulses，DMSO control。应按条件分别分析。", "preprocessing": "Max-intensity z projection；Gaussian smoothing；自定义 posterior→anterior 线；Fig1C先registration。mPSM中心对应posterior、边缘对应anterior；组织铺展与形态变化必须记录。", "missing": [ "Movie S1–S3 文件内容与大小", "Data S1/S2 是否含可复用数值表", "raw time-lapse repository", "代表图与具体实验重复的对应", "LuVeLu原始构建的完整序列/调控区需溯源Aulehla2008" ], "origin": "live", "origin_label": "真实 time-lapse", "species_label": "Mouse · 小鼠", "systems": [ "ex vivo", "embryo culture" ], "system_description": "E10.5 posterior presomitic mesoderm (PSM); explant-derived quasi-monolayer mPSM", "reporter_construct": "Axin2-T2A-Venus-PEST (Axin2T2A)：endogenous Axin2 locus；stop-codon knock-in；T2A 分隔，保留 Axin2 coding/UTR；不等于 AXIN2 蛋白量。；Axin2-T2A-Luciferase-PEST (Axin2T2A-Luci)：endogenous Axin2 locus；用于与 LuVeLu 同时成像。；LuVeLu：Lfng regulatory reporter (原构建见 Aulehla2008)；本文与 Lfng-T2A-VenusPEST knock-in 做过动力学对照。；Mesp2-GFP：Mesp2 reporter; 原构建见 Morimoto2006；固定条纹/极性标记，与钟振荡和物理边界分开。", "reported_target": "Axin2-T2A-Venus-PEST (Axin2T2A) → Axin2 / Wnt (fluorescence)；Axin2-T2A-Luciferase-PEST (Axin2T2A-Luci) → Axin2 / Wnt (bioluminescence)；LuVeLu → Lfng / Notch (fluorescence)；Mesp2-GFP → Mesp2 / segment differentiation marker (fluorescence)", "figure_focus": "Figure 1C/G：Axin2T2A / Mesp2-GFP 双通道时空图；1C胚胎、1G ex vivo。；Figure 2A/B：Axin2T2A 与 LuVeLu 两套 ex vivo kymograph；色阶各自归一化，不能直接比较颜色幅度。；Figure 6A vs 6D：6A比较振荡停止；6D brightfield比较物理边界，两个表型分开。", "replicates": "Fig2C: Axin2T2A n=10 / LuVeLu n=17; Fig2D: n=9 / n=17（已按图内柱标签视觉核实）；FigS1B: in vivo n=6, ex vivo n=21；不同分析的n不能合并。", "sources": [ { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/", "location": "Front matter / title / author list", "note": "bibliographic metadata; DOI and authors", "checked": "2026-11-09", "id": "M1" }, { "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5847172/fullTextXML", "location": "JATS; Experimental Model and Subject Details / Mouse lines", "note": "API HTTP200；164054 bytes全文XML，保存于work/mammal-sources/PMC5847172.xml。", "checked": "2026-11-09", "id": "M2" }, { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/#fig1", "location": "Figure1 C/G caption", "note": "实验kymograph、registration、70µm平均宽度。", "checked": "2026-11-09", "id": "M3" }, { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/#fig2", "location": "Figure2 A–F caption", "note": "两个reporter时空动力学；Fig2E/F才是同一样本双reporter。 Fig2C/D图内标注视觉复核：Axin2T2A=10/9，LuVeLu=17/17。", "checked": "2026-11-09", "id": "M4" }, { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/#fig6", "location": "Figure6 A/D caption", "note": "振荡停止和物理边界是不同测量。", "checked": "2026-11-09", "id": "M5" }, { "url": "https://www.sonnenlab.org/wp-content/uploads/2020/04/Sonnen_Aulehla_Cell_2018.pdf#page=15", "location": "STAR Methods / Laser scanning microscopy", "note": "10min;512×512;1.38µm/px;8µm z-step。", "checked": "2026-11-09", "id": "M6" }, { "url": "https://www.sonnenlab.org/wp-content/uploads/2020/04/Sonnen_Aulehla_Cell_2018.pdf#page=16", "location": "Generation and analysis of kymographs / Data and Software Availability", "note": "处理方法及代码需索取。", "checked": "2026-11-09", "id": "M7" }, { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/", "location": "Supplemental Information mmc1–mmc4", "note": "文件名与caption已核对；文件字节未核实为可下载。", "checked": "2026-11-09", "id": "M8" }, { "id": "R1", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5847172.1/mmc3.mp4", "location": "Official movie full decode and local ROI extraction", "note": "完整读取并解码。矩阵[354, 155]；t=[0.0, 25.69]h。取样/配准/标尺/hash见data/derived/sonnen-2018/extraction-provenance.json。8bit显示值不是raw荧光。" } ], "assets": [ { "level": "figure", "level_label": "论文图", "label": "论文图", "url": "https://www.sonnenlab.org/wp-content/uploads/2020/04/Sonnen_Aulehla_Cell_2018.pdf", "format": "PDF", "bytes": null, "size": "文件大小未核实", "status": "verified_article", "original_status": "verified_article", "evidence": "作者站全文PDF已由web工具打开；Fig1、2、6包含实验数据。", "license": "CC BY-NC-ND 4.0", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie S1 / mmc2.mp4", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5847172.1/mmc2.mp4", "format": "MP4", "bytes": 6230827, "size": "5.9 MB（PMC页面标注；未实测）", "status": "verified_content", "original_status": "blocked", "evidence": "官方PMC开放数据云文件已完整下载，PyAV全帧解码成功；H264/yuv420p为渲染视频而非raw。", "license": "CC BY-NC-ND 4.0", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie S2 / mmc3.mp4", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5847172.1/mmc3.mp4", "format": "MP4", "bytes": 10911981, "size": "10.4 MB（PMC页面标注；未实测）", "status": "verified_content", "original_status": "blocked", "evidence": "官方PMC开放数据云文件已完整下载，PyAV全帧解码成功；H264/yuv420p为渲染视频而非raw。", "license": "CC BY-NC-ND 4.0", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie S3 / mmc4.mp4", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5847172.1/mmc4.mp4", "format": "MP4", "bytes": 1315321, "size": "1.3 MB（PMC页面标注；未实测）", "status": "verified_content", "original_status": "unverified", "evidence": "官方PMC开放数据云文件已完整下载，PyAV全帧解码成功；H264/yuv420p为渲染视频而非raw。", "license": "CC BY-NC-ND 4.0", "checked": "2026-11-09" }, { "level": "document", "level_label": "补充曲线图", "label": "Data S1/S2 · PDF曲线图", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5847172.1/mmc1.pdf", "format": "PDF (Document S1: Data S1 and S2)", "bytes": 2731393, "size": "2.6 MB（PMC页面标注；未实测）", "status": "verified_content", "original_status": "unverified", "evidence": "完整PDF已读取并视觉检查；是归一化曲线图，不是可直接读取的数值表。", "license": "CC BY-NC-ND 4.0", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "原始 time-lapse", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "not_found", "evidence": "所查文章、资源表与data availability未列独立原始成像仓库。未发现不等于不存在。", "license": "CC BY-NC-ND 4.0", "checked": "2026-11-09" }, { "level": "contact", "level_label": "需要联系作者", "label": "需要联系作者", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/", "format": "MATLAB scripts", "bytes": null, "size": null, "status": "contact", "original_status": "author_statement", "evidence": "Data and Software Availability明确 scripts available upon request；此声明只明确代码，不应扩展成原始图像承诺。", "license": "CC BY-NC-ND 4.0", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "本地视频提取矩阵", "label": "探索性 ROI 强度矩阵 · movie-s2", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5847172.1/mmc3.mp4", "local_path": "data/derived/sonnen-2018/movie-s2-intensity.csv", "format": "CSV / NPZ · space × time", "bytes": 487772, "status": "verified_content", "source_is_input": true, "evidence": "本次从完整视频解码后提取；源视频、hash、逐帧平移、ROI和坐标数组均有记录。它不是作者公开的原始强度矩阵。", "license": "CC BY-NC-ND 4.0 (article/source repository); local research derivation, no publication license inferred.", "checked": "2026-11-09" } ], "recommendation": "标定完整，双pathway及停止/边界可分开；适合在取得视频/原始栈后重绘。当前文件访问受限，先不宣称数据可直接下载。", "priority": 1, "verification_scope": "正文/图注与公开方法已核；媒体附件访问受限，未核实可用原始栈或矩阵。 本轮完整解码官方视频，读取烧录时间与标尺，保存平移校正后ROI矩阵及三时点取线核查图。", "field_evidence": { "species": [ "M1", "M2" ], "system_description": [ "M1", "M2" ], "tissue": [ "M1", "M2" ], "conditions": [ "M1", "M2" ], "reporter_construct": [ "M1", "M2" ], "reported_target": [ "M1", "M2" ], "time_axis": [ "M6", "M7" ], "space_axis": [ "M6", "M7" ], "time_resolution": [ "M6", "M7" ], "space_resolution": [ "M6", "M7" ], "preprocessing": [ "M6", "M7" ], "figure_focus": [ "M3", "M4", "M5" ], "replicates": [ "M4", "M6" ], "kymograph": [ "R1" ] }, "short": "Sonnen 2018", "reporter_short": "Axin2T2A · LuVeLu · Mesp2-GFP", "reporter_tags": [ "Axin2T2A", "LuVeLu", "Mesp2-GFP" ], "patterns": [ "振荡传播波", "振荡停止", "固定表达条纹", "形态学 somite boundaries" ], "time_axis": "Fig2A/B横轴时间h，标注0–20；Fig1C/G同为time–space表示。", "space_axis": "Fig2A/B纵轴距离µm，标注0–200；ex vivo取样从mPSM中心（posterior）到边缘（anterior）。", "time_resolution": "荧光10 min/frame；同步生物发光每10 min（9 min曝光 + 10 s LuVeLu）。 本次MovieS2逐帧烧录时间已读取：155帧，0–25.69h，显示精度0.01h；使用时间数组，不由播放FPS推断。", "space_resolution": "激光扫描1.38 µm/pixel，512×512，z-step8 µm；Fig1 kymograph沿50px≈70µm宽线平均。生物发光像素尺度未核实。 MovieS2重绘采用100µm/139视频像素（≈0.719µm/px），来自画面标尺，不能直接套1.38µm原像素。", "summary": "Wnt / Notch 波速、相位差与振荡停止；时空标定最完整，适合作为先试候选。", "calibration_short": "逐帧时间戳 · 视频标尺已核", "availability_status": "verified_content", "availability_summary": "官方视频已解码 · 已提取探索性ROI矩阵；原始成像栈未定位。", "availability_filters": [ "论文图已核实", "补充视频列出 / 待验证", "代码需联系作者", "视频已解码", "本地提取矩阵" ], "caveats": [ "Fig2A与2B来自不同reporter实验；Fig2E/F才是同一样本双reporter。", "两套伪彩色色阶分别归一化，不能直接比较荧光幅值。", "Data S1/S2在PDF中，未证实为机器可读数值矩阵；MATLAB索取声明只承诺代码。", "Mesp2固定表达条纹、振荡停止和brightfield边界为不同表型。", "新增本地重绘来自压缩视频；仅平移校正，不是组织形变/细胞追踪。不同reporter绝对亮度不可比较。" ], "media": [ { "label": "Figure 2 · Wnt / Notch spatiotemporal dynamics", "url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/19c3/5847172/ad27c7fd4588/gr2.jpg", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/#fig2", "description": "A/B是两套实验kymograph；E/F为同一样本的双reporter。完整原图保留，不裁剪或重绘。", "attribution": "Sonnen et al., Cell (2018), Figure 2. DOI:10.1016/j.cell.2018.01.026. CC BY-NC-ND 4.0.", "status": "已在实际Chrome看板加载原图：749×853 px；仅为论文图，非原始成像。" } ], "checked": "2026-11-09", "kymograph": { "kind": "experimental", "short": "Kymograph · 原图 / 视频重绘", "selector": "原图 / 视频重绘", "order": 2, "preview": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/19c3/5847172/ad27c7fd4588/gr2.jpg", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/#fig2", "panel": "Fig. 2A / B · Wnt × Notch", "panel_note": "A/B 为两组实验；E/F 为同一样本的双 reporter。完整原图。", "attribution": "Sonnen et al., Cell (2018), Figure 2. DOI:10.1016/j.cell.2018.01.026. CC BY-NC-ND 4.0.", "focus": "两条通路的相位关系", "takeaway": "适合对照多基因模型的传播波与相位差。E/F 可观察同一样本的双 reporter。", "reporter": "Axin2T2A · LuVeLu", "time": "横轴 t · h（A/B：0–20）", "space": "纵轴位置 · µm（A/B：0–200）", "signal": "各自归一化荧光强度", "metrics": [ "波向", "相位差", "周期" ], "limit": "10 min / frame · 1.38 µm / px。两通道色阶不可直接作幅度比较。", "model_note": "分别定义Wnt/Notch通道的观测映射。先比较周期与相对相位；振荡停止与形态边界需再对照原文Fig6的不同面板。", "comparison": { "id": "sonnen-2018", "short": "Sonnen 2018", "reporter": "Axin2T2A", "kind": "video", "label": "Video-derived ROI", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/", "origin": "ROI start → periphery", "origin_short": "ROI 起点 → 外缘", "sample": "movie-s2", "position_unit": "µm", "roi": "figures/sonnen-2018/movie-s2-roi.jpg", "input": "data/derived/sonnen-2018/movie-s2-kymograph.npz", "input_sha256": "d11b72d3b4bfcdb7b89132dcf4c2b72d992399a911d53b6e60f8bc4261234ab2", "shape_space_time": [ 354, 155 ], "time_range_h": [ 0.0, 25.69 ], "spatial_range": [ 0.0, 254.55835989862058 ], "missing_values": 0, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 52.668596285793306, "max": 239.13408927284533 }, "spatial_range_um": [ 0.0, 254.55835989862058 ], "common_preview": "figures/comparison/sonnen-2018-common.svg", "full_preview": "figures/comparison/sonnen-2018-full.svg" }, "rendered": { "intensity": { "preview": "figures/sonnen-2018/video-intensity.svg", "source_url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC5847172.1/mmc3.mp4", "panel": "Movie S2 · Axin2T2A 视频提取", "panel_note": "354×155 · 平移校正 · 宽线平均", "attribution": "Sonnen 2018 · 官方补充视频。Clock Explorer 独立取样重绘；不是原论文面板或原始荧光矩阵。", "focus": "从视频恢复时空波形", "takeaway": "去除字幕区域，以平移校正后的 ROI 逐帧取样。完整取样路径可核查。", "reporter": "Axin2T2A · 小鼠", "time": "横轴 · h；逐帧画面时间戳", "space": "纵轴 · 距 ROI 起点 µm（近似）", "signal": "8-bit 视频显示值 · 非原始荧光计数", "limit": "压缩视频 + 平移校正；未校正组织形变。用于定性波形比较，不能据此比较绝对幅值。", "model_note": "源视频已完整解码。Lauschke使用匹配明场Video4估计平移；Sonnen使用自身灰度纹理估计平移。沿预先记录的直线ROI做双线性取样和横向均值；不做时间平滑、去趋势或phase推断。空间尺度从100µm视频标尺测量，不能套原相机像素尺度。此ROI不宣称复制原论文取线；位置不是共同解剖坐标。", "downloads": { "svg": "figures/sonnen-2018/video-intensity.svg", "pdf": "figures/sonnen-2018/video-intensity.pdf", "png": "figures/sonnen-2018/video-intensity.png" }, "roi_preview": "figures/sonnen-2018/movie-s2-roi.jpg", "metrics": [ "传播方向", "波形", "组织漂移" ] } }, "card_context": { "condition": "离体 mPSM", "sample": "Movie S2", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/", "evidence": "Movie S2 caption identifies the Axin2T2A ex vivo cell culture assay. The 37°C microfluidic protocol is not assigned to this non-microfluidic movie." } } }, { "id": "delaune-2012", "title": "Single-Cell-Resolution Imaging of the Impact of Notch Signaling and Mitosis on Segmentation Clock Dynamics", "authors": [ "Emilie A. Delaune", "Paul François", "Nathan P. Shih", "Sharon L. Amacher" ], "year": 2012, "doi": "10.1016/j.devcel.2012.09.009", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3500528/", "species": "Danio rerio", "tissue": "PSM; whole zebrafish embryo mounted laterally", "conditions": "Heterozygous reporter; WT, bea/deltaC, des/notch1a, aei/deltaD; 22–23°C; beginning at 8–12 somites for 4–6 h", "reporter_construct": "Tg(her1:her1-Venus)bk15: 8.6 kb her1 upstream region → C-terminal Her1–Venus fusion → 1.1 kb her1 downstream/3′UTR sequence", "reported_target": "her1 regulatory activity and unstable nuclear Her1–Venus fusion protein; not a direct her1 mRNA concentration measurement", "figure_focus": "Fig.1F / Movie S1 tissue waves; Fig.2D–F single-cell intensity/phase; Fig.3 traces and neighbor phase; processed movies include tracking/phase overlays.", "time_axis": "minutes; stacks every 4 min; 4–6 h total; do not use video playback FPS as biological time", "space_axis": "A–P tissue position; Methods: 2.092 pixels/µm; z-step 1.34 µm", "replicates": "3 WT embryos, 50–100 tracked/validated cells per movie; Fig.3J–M shows 3 embryos per genotype", "caveats": [ "No decodable experimental media or cell-intensity matrix obtained. No synthetic matrix or reconstruction from paper stills produced.", "Original acquisition 2.092 pixels/µm and z-step1.34µm do not calibrate a rendered movie that has not been acquired." ], "sources": [ { "id": "S1", "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=3500528&retmode=xml", "location": "Live imaging; Supplementary Material SD2–SD4", "note": "Full JATS obtained; original acquisition documented." }, { "id": "S2", "url": "https://pmc-oa-opendata.s3.amazonaws.com/?list-type=2&prefix=PMC3500528", "location": "Official public object inventory", "note": "Only 3 objects:metadata JSON,TXT,XML. No images,video,or numerical matrix." }, { "id": "S3", "url": "https://pmc.ncbi.nlm.nih.gov/tools/cloud/", "location": "Files,author manuscripts", "note": "Non-CC author-manuscript PDFs/media/supplementary files not included in PMC data service." } ], "field_evidence": { "conditions": [ "S1", "S2", "S3" ], "time_resolution": [ "S1", "S2", "S3" ], "reporter_construct": [ "S1", "S2", "S3" ] }, "recommendation": "生物问题与 Paul 的既有工作高度贴近，标定完整；适合作为第二候选，但应先解决补充视频/矩阵访问。", "species_label": "Zebrafish · 斑马鱼", "systems": [ "in vivo" ], "system_description": "in vivo; confocal live imaging", "assets": [ { "level": "figure", "level_label": "论文图", "label": "Fig.1–3 preview via PubMed", "url": "https://pubmed.ncbi.nlm.nih.gov/23153496/#&gid=article-figures&pid=figure-1-uid-0", "format": "web figure", "bytes": null, "size": null, "status": "verified_article", "original_status": "article_caption_verified", "evidence": "PubMed figure captions available; no local image copied", "license": "© 2012 Elsevier, all rights reserved; PMC manuscript text-mining/fair-use statement is not CC image license", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie S1 (SD2; NIHMS417414-supplement-02.avi)", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3500528/bin/NIHMS417414-supplement-02.avi", "format": "AVI", "bytes": null, "size": null, "status": "restricted", "original_status": "access_challenge", "evidence": "JATS explicitly maps Movie S1 to SD2. HEAD returned HTTP 200 text/html (size 0), not AVI; download not verified.", "license": "© 2012 Elsevier; separate reuse permission not established", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "SD3 (NIHMS417414-supplement-03.avi)", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3500528/bin/NIHMS417414-supplement-03.avi", "format": "AVI", "bytes": null, "size": null, "status": "restricted", "original_status": "access_challenge", "evidence": "Listed in JATS; HEAD HTTP 200 text/html, not AVI. Exact included movie range not resolved.", "license": "© 2012 Elsevier; separate reuse permission not established", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "SD4 (NIHMS417414-supplement-04.mov)", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3500528/bin/NIHMS417414-supplement-04.mov", "format": "MOV", "bytes": null, "size": null, "status": "restricted", "original_status": "access_challenge", "evidence": "Listed in JATS; HEAD HTTP 200 text/html, not MOV. Fig.3 references Movies S2–S9, but file grouping not resolved.", "license": "© 2012 Elsevier; separate reuse permission not established", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "强度 / kymograph 矩阵", "label": "Tracked cell fluorescence/position matrix", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "not_located", "evidence": "Methods states such a matrix was constructed; no public matrix repository found in inspected article. Author contact may be needed, not performed.", "license": "unknown", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "Multichannel confocal z-stacks", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "not_located", "evidence": "Acquisition described; no public raw-stack deposit located in inspected article.", "license": "unknown", "checked": "2026-11-09" }, { "level": "contact", "level_label": "需要联系作者", "label": "MATLAB tracking/analysis program", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3500528/", "format": "MATLAB", "bytes": null, "size": null, "status": "contact", "original_status": "author_request_stated", "evidence": "Article front matter directs MATLAB-program requests to Paul François. No request sent; data availability not implied.", "license": "unknown", "checked": "2026-11-09" } ], "priority": 2, "short": "Delaune 2012", "journal": "Developmental Cell", "origin": "live", "origin_label": "真实 time-lapse", "patterns": [ "振荡传播波", "振荡停止", "形态学 somite boundaries" ], "reporter_short": "Her1–Venus", "reporter_tags": [ "Her1–Venus" ], "time_resolution": "4 min/frame；总长4–6 h。", "space_resolution": "2.092 pixels/µm → 约0.478 µm/pixel（倒数换算）；z-step 1.34 µm。不是光学分辨率；导出视频可能缩放。", "summary": "单细胞跟踪连接 Notch 同步、细胞分裂与 Her1 振荡；Paul François 共同第一作者。", "calibration_short": "4 min · 0.478 µm/px", "availability_status": "restricted", "availability_summary": "未取得可重绘时间序列", "availability_filters": [ "正文 / 索引已核", "数值矩阵未取得" ], "verification_scope": "本轮已核公开附件与仓库访问；未取得可解码影片或连续强度矩阵。", "preprocessing": "核追踪得到每个细胞的荧光与空间轨迹，人工核验50–100细胞/胚胎；相位色图是加工结果。组织A–P位置与随细胞移动坐标需区分。", "missing": [ "The actual time-lapse confocal stacks or an officially supplied complete rendered movie", "Frame timestamps and movie resizing/cropping information", "Per-cell intensity/position matrix for reproducing tracking analyses" ], "media": [ { "label": "Fig.1F / Movie S1 tissue waves; Fig.2D–F single-cell intensity/phase; Fig.3 traces and neighbor phase; processed movies include tracking/phase overlays.", "url": null, "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3500528/", "description": "未嵌入实验图；通过原文图号/补充链接查看。", "status": "没有经核实且允许复用的图像/视频内嵌预览。" } ], "checked": "2026-11-09", "kymograph": { "kind": "traces", "short": "单细胞轨迹 · 非二维 kymograph", "preview": null, "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3500528/", "note": "Fig1F组织波；Fig2D–F及Fig3为单细胞强度/相位轨迹。未在已核图中定位二维实验kymograph。" } }, { "id": "soroldoni-2014", "short": "Soroldoni 2014", "title": "A Doppler effect in embryonic pattern formation", "authors": [ "Daniele Soroldoni", "David J. Jörg", "Luis G. Morelli", "David L. Richmond", "Johannes Schindelin", "Frank Jülicher", "Andrew C. Oates" ], "year": 2014, "journal": "Science", "doi": "10.1126/science.1253089", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7611034/", "species": "Danio rerio", "species_label": "Zebrafish · 斑马鱼", "systems": [ "in vivo" ], "system_description": "多胚胎同步活体time-lapse；遗传信号与形态分节共同观察。", "tissue": "胚胎 trunk PSM，从posterior到anterior", "conditions": "每次20个xy位置；z-stack 6×20 µm。精确温度/帧间隔需补充方法核对。", "reporter_construct": "Looping transgenic her1 reporter；Her1::YFP fusion protein。完整cassette见FigS1，本次未核实其序列/UTR。", "reported_target": "her1表达调控与Her1::YFP融合蛋白；不是mRNA浓度的直接观测。", "reporter_short": "Looping · Her1::YFP", "reporter_tags": [ "Her1::YFP" ], "origin": "live", "origin_label": "真实 time-lapse", "patterns": [ "振荡传播波", "振荡停止", "形态学 somite boundaries" ], "figure_focus": "Fig1B/C/D：实时表达波与前后ROI；Fig2A：实验强度kymograph，2C：其派生phase map；Fig3为Doppler示意。", "time_axis": "Fig2A/C纵轴time [min]；每横行对应一个时刻。原图轴已在Chrome核对，帧间隔仍未核实。", "space_axis": "Fig2A/C横轴PSM length [µm]；左posterior、右anterior。沿完整PSM的LOI，每行长度随PSM缩短。", "time_resolution": "未知：补充方法PDF未完成读取；不能用video FPS或ROI文件序号猜测。", "space_resolution": "Fig1B scale bar100 µm；z-step20 µm ×6；XY µm/pixel未知。", "replicates": "Fig1E: N=4独立实验，n=40胚胎；Fig2D: N=2，n=18胚胎。Fig2A/C为单代表胚胎。", "preprocessing": "ROI/LOI interpolator随组织取样；强度kymograph经wavelet变换提取phase。固定像素、组织坐标和PSM相对长度不可混为一谈。", "summary": "直接展示PSM缩短下的传播波与Doppler效应；公开ZIP只有ROI/LOI标注。", "calibration_short": "标尺100 µm · 间隔待核", "availability_status": "verified_content", "availability_summary": "ZIP 已打开 · 仅 ROI / LOI", "availability_filters": [ "论文图已核实", "ROI标注文件已读取", "数值矩阵未定位" ], "priority": 5, "caveats": [ "仓库“Dataset”标签不等于包含raw images；本次ZIP只发现ImageJ ROI/LOI及嵌套ZIP。", "Fig2相位图来自实验强度；Fig3机制示意不能当实验。", "PSM明显缩短；归一化x/L会改变表观波速，需同时保留物理坐标。" ], "recommendation": "适合形态与波传播比较的第三候选。已可取得ROI/LOI标注，但缺对应图像与时间标定；拿到匹配序列后可沿作者LOI重建Fig2A。", "missing": [ "对应ROI的原始成像序列", "processed intensity matrix", "帧间隔与XY像素标定", "movie文件实际入口与内容", "Looping完整cassette" ], "verification_scope": "NCBI BioC全文、机构PDF/补充页面、Zenodo API和351534-byte ZIP均已读取；未取得raw imaging。", "media": [ { "label": "Figure 2A/C · 实验强度 / 推导相位", "url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/afb0/7611034/ae8a12d34160/EMS127446-f002.jpg", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7611034/#F2", "description": "A：实验强度时空图；C：由实验强度导出的 phase map。", "attribution": "Soroldoni et al. · Science 345, 222–225 (2014) · DOI 10.1126/science.1253089 · PMC author manuscript Fig. 2. 未确认开放再利用许可；原来源加载。", "status": "2026-11-09已在实际Chrome原文页面核对图注和图片src；按需加载完整原图。" } ], "sources": [ { "id": "S1", "url": "https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_xml/PMC7611034/unicode", "location": "Results; Fig1 and Fig2 captions", "note": "HTTP200 XML全文，实际读取；构建、LOI、n与标尺。", "checked": "2026-11-09" }, { "id": "S2", "url": "https://www.pks.mpg.de/fileadmin/user_upload/MPIPKS/group_pages/BiologicalPhysics/juelicher/publications/2014/ADEiEPF2014.pdf", "location": "Author institution-hosted Science article", "note": "HTTP200 PDF,603346 bytes；仅个人研究阅读，不假定CC许可。", "checked": "2026-11-09" }, { "id": "S3", "url": "https://publications.mpi-cbg.de/5812-site", "location": "Supplementary Data", "note": "机构页面链接Zenodo concept DOI10.5281/zenodo.21916315。", "checked": "2026-11-09" }, { "id": "S4", "url": "https://zenodo.org/api/records/21916316", "location": "files[0]; metadata.license; related_identifiers", "note": "351534 bytes，md5:0e44051324af84f751881b4cea58cec1；CC BY4.0；isSupplementTo目标论文。", "checked": "2026-11-09" }, { "id": "S5", "url": "https://zenodo.org/records/21916316", "location": "6_roi_loi sets.zip archive inventory", "note": "HTTP200实下351534 bytes；逐层ZIP检查为.roi与目录/元数据，未发现像素影像或强度矩阵；核查日期2026-11-09。", "checked": "2026-11-09" }, { "id": "K1", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7611034/#F2", "location": "Figure 2A/C · 实验强度 / 推导相位；实际Chrome网页", "note": "A：实验强度时空图；C：由实验强度导出的 phase map。", "access": "图注及原图链接已核；未下载原始成像数据" } ], "field_evidence": { "species": [ "S1" ], "system_description": [ "S1" ], "tissue": [ "S1" ], "conditions": [ "S1" ], "reporter_construct": [ "S1" ], "reported_target": [ "S1" ], "figure_focus": [ "S1" ], "time_axis": [ "K1" ], "space_axis": [ "K1" ], "space_resolution": [ "S1" ], "replicates": [ "S1" ], "preprocessing": [ "S1" ], "kymograph": [ "K1" ] }, "assets": [ { "level": "figure", "level_label": "论文图", "label": "Figures 1–2 / author-hosted article", "url": "https://www.pks.mpg.de/fileadmin/user_upload/MPIPKS/group_pages/BiologicalPhysics/juelicher/publications/2014/ADEiEPF2014.pdf", "format": "PDF", "bytes": 603346, "status": "verified_content", "evidence": "机构公开PDF已获取；图注另由BioC全文核对。", "license": "©2014 AAAS；未核实开放复用许可" }, { "level": "annotation", "level_label": "ROI / LOI 标注", "label": "6_roi_loi sets.zip — 仅ImageJ取样标注", "url": "https://zenodo.org/api/records/21916316/files/6_roi_loi%20sets.zip/content", "format": "ZIP containing ImageJ .roi / nested ZIP", "bytes": 351534, "status": "verified_content", "evidence": "GET200；已打开外层及嵌套ZIP目录；没有原始像素强度。仓库于2026-08-13建立，publication_date回填2014-07-11。", "license": "CC BY4.0（Zenodo metadata）" }, { "level": "movie", "level_label": "补充视频", "label": "Movies S1–S5（正文引用）", "url": "https://www.science.org/doi/10.1126/science.1253089", "format": "未知", "bytes": null, "status": "listed", "evidence": "正文引用movies；本次没有读取实际电影文件。", "license": "未知" }, { "level": "matrix", "level_label": "强度 / kymograph 矩阵", "label": "LOI intensity matrix", "url": null, "format": null, "bytes": null, "status": "unknown", "evidence": "已读仓库内容只有ROI标注，数值矩阵未定位。", "license": "未知" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "与ROI匹配的原始影像", "url": null, "format": null, "bytes": null, "status": "unknown", "evidence": "未在已查机构页面/Zenodo记录找到原始栈。", "license": "未知" } ], "checked": "2026-11-09", "kymograph": { "kind": "experimental", "short": "Kymograph · Fig. 2A / C", "selector": "斑马鱼 · 强度 / 相位", "order": 3, "preview": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/afb0/7611034/ae8a12d34160/EMS127446-f002.jpg", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7611034/#F2", "panel": "Fig. 2A / C · 强度与相位", "panel_note": "A：实验强度时空图；C：由实验强度导出的 phase map。", "attribution": "Soroldoni et al. · Science 345, 222–225 (2014) · DOI 10.1126/science.1253089 · PMC author manuscript Fig. 2. 未确认开放再利用许可；原来源加载。", "focus": "组织缩短与波形变化", "takeaway": "更接近斑马鱼体内的实时对照。可一起查看波形、停止端移动与局部波长。", "reporter": "Looping · Her1::YFP", "time": "纵轴 t · min", "space": "横轴 PSM 长度 · µm；左后→右前", "signal": "A：强度；C：推导相位", "metrics": [ "波向", "局部波长", "停止端移动" ], "limit": "坐标方向与 Lauschke 相反。ROI 标注已获取；原始影像与数值矩阵未获取。", "model_note": "先统一时间/空间轴方向，再把组织长度变化与振荡动力学分开。停止端的位置随时间变化，不能只比较固定像素处的周期。" } }, { "title": "Self-Organization of Embryonic Genetic Oscillators into Spatiotemporal Wave Patterns", "authors": [ "Charisios D. Tsiairis", "Alexander Aulehla" ], "year": 2016, "journal": "Cell 164(4):656–667", "doi": "10.1016/j.cell.2016.01.028", "reporter_construct": "LuVeLu transgene：Lfng/lunatic fringe promoter → Venus (YFP)；本篇正文未重述完整cassette、降解标签与UTR，补充方法PDF本次未能打开，因此不补写。Mesp2-GFP为另一个分化reporter；H2B-mCherry为细胞身份/定位标签。", "reported_target": "主要：Lfng promoter activity，作为Notch signaling dynamics的间接读数；不是Notch蛋白浓度或所有GRN基因的表达量。另：Mesp2 activation标记分化/segmentation program启动。", "conditions": "重聚实验每组6个胚胎PSM；fibronectin-coated coverglass，最长24 h，37°C，5% CO2；对照及2 µM DAPT；另有仅tail-bud细胞、FACS相位分选与前/后PSM混合条件。", "missing": [ "Movie S1/S2实际视频文件（PMC所链是.jpg，不应标为已确认可下载movie）", "原始time-lapse stack和数值kymograph matrix仓库", "采样间隔、µm/pixel、原始强度单位、原图kymograph轴刻度", "Fig1D/G对应的独立生物重复数", "LuVeLu完整cassette与补充方法PDF内容" ], "sources": [ { "id": "T1", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/", "location": "header; Copyright and License; Footnotes", "supports": "title/authors/date/DOI；CC BY4.0", "access": "web全文实际打开；本地HTTP GET返回203检查页，因此正文核查依据web返回内容", "checked": "2026-11-09" }, { "id": "T2", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/#fig1", "location": "Figure1 legend B–H；Results: Randomized PSM Cell Populations Self-Organize in Space and Time", "supports": "LuVeLu=L f n g promoter/Venus；实验kymograph1D/G；n=3/control与DAPT；2 µM DAPT；5–6 h同步建立", "access": "text verified", "checked": "2026-11-09" }, { "id": "T3", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/#fig3", "location": "Figure3 legend F–H; Figure2F/G; FigureS3A", "supports": "3G tail-bud-only kymograph；Mesp2身份；完整PSM n=8", "access": "text verified", "checked": "2026-11-09" }, { "id": "T4", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/", "location": "Experimental Procedures — Embryo PSM Culture and Randomization Assays", "supports": "six pooled PSM；fibronectin；24 h、37°C、5% CO2", "access": "text verified", "checked": "2026-11-09" }, { "id": "T5", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/", "location": "Experimental Procedures — Imaging and Image Processing / Quantifications", "supports": "Fiji lines/ROIs、Hilbert phase、Fourier；成像方法引用Lauschke2013而非本篇重述", "access": "text verified", "checked": "2026-11-09" }, { "id": "T6", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/", "location": "Supplemental Information; Associated Data", "supports": "MovieS1–S5说明；E10.5、hr:min；列出的实际附件名称与文件大小；DocumentS1", "access": "listing verified; linked binaries not verified", "checked": "2026-11-09" }, { "id": "K1", "url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e669/4752819/a6c114cabe52/gr1.jpg", "location": "Figure1完整原图，2026-11-09 Chrome视觉核对", "note": "D/G无数值轴；H为Time(min)。D/G取样线在C/F，不用H坐标替代。", "access": "图片可见" }, { "id": "R1", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC4752819.1/mmc1.pdf", "location": "Supplementary Methods page 2", "note": "PDF全文读取及页面视觉核对：10min采集间隔；mmc2/3实际为单帧JPEG，不是视频。" } ], "id": "tsiairis-2016", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/", "short": "Tsiairis 2016", "species": "Mus musculus", "species_label": "Mouse · 小鼠", "systems": [ "ex vivo", "in vitro" ], "system_description": "E10.5 mouse PSM；完整tail-bud的2D explant/mPSM，与解离后随机重聚的ePSM并行比较", "tissue": "E10.5 PSM / tail bud；mPSM explant 与 ePSM re-aggregates", "origin": "live", "origin_label": "真实 time-lapse", "reporter_short": "LuVeLu · Mesp2-GFP", "reporter_tags": [ "LuVeLu", "Mesp2-GFP" ], "patterns": [ "振荡传播波", "振荡停止", "单细胞振荡" ], "summary": "重聚细胞自发建立多个波源；适合研究同步化，但实际视频与像素标定仍待补。", "calibration_short": "10 min · 视频仍未取得", "time_axis": "Fig1D/G原图没有数值时间刻度；Fig1H横轴Time(min)，不借用H的刻度标定D/G。Movie S1–S5图注明确hr:min；采样间隔仍未知。", "space_axis": "Fig1D/G原图没有距离数值刻度；黄色箭头对应C/F取样方向：D由mPSM中心向周边，G跨两个ePSM波源。", "time_resolution": "补充Methods已核：每10 min采集z-stack；未取得可解码实验视频。", "space_resolution": "补充Methods：20× NA0.8，3–4层z-stack，z间距3–5µm。视频像素尺度未核实；不能从单帧预览迁移到未取得的视频。", "replicates": "Fig1H同步幅度对照与DAPT各n=3；FigS3A完整PSM频率梯度n=8；Fig1D/G示例kymograph对应独立生物重复数未明确。6个胚胎为每次重聚的pool大小，不是6个独立重复。", "figure_focus": "Fig1D/G、3G是从真实time-lapse计算的实验kymograph；2D径向波从中心传播到周边，ePSM有多个波源。周边振荡停止与Mesp2启动不应直接等同于形态学somite boundaries。Fig1A、3A/D、5A/B含示意图；FigS1随机foci分布是模拟对照。", "preprocessing": "Fiji沿黄色线取样；Hilbert transform求相位，Fourier分析周期。中心/边缘运动与多foci需分别配准。", "recommendation": "适合检验多波源、同步化与径向频率梯度。完整tail-bud Movie S1比多foci的Movie S2更适合作为一维x(t,p)的初始对照，但必须先取得实际视频及标定。 先取得S1的真实视频/原始stack和采样间隔，选定中心与稳定径向ROI，背景扣除，生成I(t,r)；保留原物理尺度与归一化r/R两套坐标，再与模型并排观察波向、周期梯度和arrest。当前附件访问和标定缺口使其不宜排在第一位。", "assets": [ { "level": "figure", "level_label": "论文图", "label": "正文及实验图图注", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/#fig1", "format": "HTML figure/caption", "bytes": null, "size": null, "status": "verified_article", "original_status": "verified_article_text", "evidence": "web全文实际打开；Figure1D/G图注明确为kymograph。图片文件和像素本次未取得。", "license": "Article CC BY 4.0；保留作者、论文、图号和链接署名。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie S1 — 2D explant；PMC显示mmc2.jpg", "url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/4752819/bin/mmc2.jpg", "format": "jpg (page listing); actual movie format unknown", "bytes": null, "size": "392.7 KB (article listing, not measured)", "status": "format_mismatch", "original_status": "article_claim_only_file_fetch_failed", "evidence": "Movie图注与链接已读；点击返回Cache miss，未得到视频。jpg不能标为time-lapse视频下载。 本轮官方S3下载并用PIL确认单帧JPEG；不能据此构造实测时间序列。", "license": "CC BY 4.0 article；补充文件单独版权声明未打开核对。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie S2 — 6 embryo PSM re-aggregation；PMC显示mmc3.jpg", "url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/4752819/bin/mmc3.jpg", "format": "jpg (page listing); actual movie format unknown", "bytes": null, "size": "494.2 KB (article listing, not measured)", "status": "format_mismatch", "original_status": "article_claim_only_access_challenge", "evidence": "Movie图注与链接已读；点击返回reCAPTCHA，未得到文件；不是确认失效。 本轮官方S3下载并用PIL确认单帧JPEG；不能据此构造实测时间序列。", "license": "CC BY 4.0 article；补充文件单独版权声明未打开核对。", "checked": "2026-11-09" }, { "level": "document", "level_label": "补充文档", "label": "Document S1 / Supplemental Experimental Procedures", "url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/4752819/bin/mmc1.pdf", "format": "PDF (article listing)", "bytes": null, "size": "70.3 KB (article listing, not measured)", "status": "restricted", "original_status": "access_challenge", "evidence": "正文给出文件链接与大小；web点击返回reCAPTCHA，没有打开PDF内容。", "license": "CC BY 4.0 article；文件单独声明未知。", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "强度 / kymograph 矩阵", "label": "可重画的数值矩阵", "url": null, "format": "unknown", "bytes": null, "size": null, "status": "unknown", "original_status": "not_found_in_checked_sources", "evidence": "正文Associated Data只列supplemental documents/movies；本次题名/DOI公开检索未定位数值矩阵仓库，不等于证明不存在。", "license": "unknown", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "原始显微成像序列", "url": null, "format": "unknown", "bytes": null, "size": null, "status": "unknown", "original_status": "unverified", "evidence": "本次核查未找到raw imaging accession；补充展示视频即使可播放也不能当作raw图像stack。后续可核对出版社附件，仍缺失再讨论联系作者。", "license": "unknown", "checked": "2026-11-09" } ], "field_evidence": { "species": [ "T1", "T6" ], "tissue": [ "T4" ], "conditions": [ "T4" ], "system_description": [ "T4" ], "reporter_construct": [ "T2", "T3" ], "reported_target": [ "T2", "T3" ], "figure_focus": [ "T2", "T3" ], "time_axis": [ "K1" ], "space_axis": [ "K1" ], "time_resolution": [ "R1" ], "space_resolution": [ "R1" ], "replicates": [ "T2", "T3", "T4" ], "preprocessing": [ "T5" ] }, "priority": 6, "availability_status": "format_mismatch", "availability_summary": "“Movie” 入口是 JPG · 视频未核实", "availability_filters": [ "论文图已核实", "补充视频列出 / 待验证", "格式不符", "数值矩阵未定位" ], "verification_scope": "正文/图注/附件清单已核，真实浏览器读到Fig1原图src；movie实际链接为jpg。", "caveats": [ "Fig1A是示意图；Fig1D/G与3G才是实验kymograph。", "每次6胚胎pool不等于6个独立生物重复。", "Mesp2启动标记分化程序，不等同于已经形成形态学somite boundaries。", "LuVeLu读数包含reporter动力学，不能直接映射任意GRN节点。" ], "media": [ { "label": "Figure 1D, 1G", "url": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e669/4752819/a6c114cabe52/gr1.jpg", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/#fig1", "description": "完整tail-bud mPSM与随机重聚ePSM的实验时空波；1D沿1C黄色箭头，1G沿1F黄色箭头跨两个foci。 完整Figure1包含A示意图；D/G为实验。", "attribution": "Tsiairis CD & Aulehla A. Cell (2016), Figure 1. DOI:10.1016/j.cell.2016.01.028. CC BY 4.0.", "status": "PMC原图src由真实浏览器读取；远程按需预览。" } ], "checked": "2026-11-09", "kymograph": { "kind": "experimental", "short": "Kymograph · Fig. 1D / G", "selector": "重聚组织 · 多波源", "order": 4, "preview": "https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e669/4752819/a6c114cabe52/gr1.jpg", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4752819/#fig1", "panel": "Fig. 1D / G · 自组织波", "panel_note": "D：mPSM；G：跨重聚 ePSM 两个波源。A 为示意图。", "attribution": "Tsiairis CD & Aulehla A. Cell (2016), Figure 1. DOI:10.1016/j.cell.2016.01.028. CC BY 4.0.", "focus": "局部振荡如何形成组织波", "takeaway": "对照正常组织与重聚细胞的波形，适合考察网络的同步与自组织能力。", "reporter": "LuVeLu · 小鼠", "time": "D/G 未标数值刻度；H 为 min", "space": "沿 C/F 黄色取样线；D/G 无距离刻度", "signal": "实验 reporter 强度", "metrics": [ "波源", "同步", "空间组织" ], "limit": "D/G 用于定性对照；不能借用 H 的坐标或标尺直接计算传播速度。", "model_note": "模型应对应取样几何：D沿中心→周边，G跨两个波源。单条一维A–P模型不能直接等同于整个二维重聚培养。" } }, { "id": "masamizu-2006", "title": "Real-time imaging of the somite segmentation clock: Revelation of unstable oscillators in the individual presomitic mesoderm cells", "authors": [ "Yoshito Masamizu", "Toshiyuki Ohtsuka", "Yoshiki Takashima", "Hiroki Nagahara", "Yoshiko Takenaka", "Kenichi Yoshikawa", "Hitoshi Okamura", "Ryoichiro Kageyama" ], "year": 2006, "journal": "Proceedings of the National Academy of Sciences", "doi": "10.1073/pnas.0508658103", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/", "species": "Mus musculus", "tissue": "E10.5 caudal embryo / PSM; dissected PSM fragments; dissociated PSM cells; C3H10T1/2 fibroblasts as comparator", "conditions": "E10.5 小鼠尾部 / PSM 离体培养；37°C、5% CO₂、85% O₂，100% rat serum + 1 mM luciferin。文中组织成像持续15 h，周期约160 min；本地补充视频解码45帧。", "preprocessing": "手工ROI，随细胞移动调整；扣除无细胞区背景，去cosmic-ray噪声；正文说数据记录于Excel，但未找到公开Excel文件。", "missing": [ "PSM空间µm/px标定", "组织级生物重复n", "原始成像及ROI Excel", "精确frame间隔", "明确再利用许可" ], "origin": "live", "origin_label": "真实 time-lapse", "species_label": "Mouse · 小鼠", "systems": [ "ex vivo", "in vitro" ], "system_description": "E10.5 caudal embryo / PSM; dissected PSM fragments; dissociated PSM cells; C3H10T1/2 fibroblasts as comparator", "reporter_construct": "Hes1-Ub1-Luc：2.5-kb Hes1 promoter + 5′/3′ UTR；N-terminal ubiquitin G76V fused firefly luciferase；PSM使用此transgenic reporter，报告promoter activity，非HES1蛋白浓度。；Hes1-Ub2-Luc：Hes1 promoter；双ubiquitin；主要fibroblast实验，不能混作PSM数据。", "reported_target": "Hes1-Ub1-Luc → Hes1 / Notch-related cyclic gene / Hes1 negative feedback (bioluminescence)；Hes1-Ub2-Luc → Hes1 / Notch-related cyclic gene (bioluminescence)", "figure_focus": "Figure 3a/b：PSM从caudal向S0传播；图3a序列、3b ROI时间曲线，不是已公开二维数值矩阵。；Figure 3c：brightfield；15h后6对新体节。；Figure 5 / Figure 8：耦合随机振子时空图，不能当实验kymograph。", "replicates": "Fig3代表PSM组织的胚胎n未核实；Fig2 fibroblast n=48不是组织重复。", "sources": [ { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/", "location": "Front matter; Fig1 / Plasmids", "note": "metadata与reporter构建；cached source可读，直接页面受captcha。", "checked": "2026-11-09", "id": "M1" }, { "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=1345707&retmode=xml", "location": "PMC front matter XML", "note": "HTTP200,8988 bytes；只返回front matter/摘要/版权，非全文。", "checked": "2026-11-09", "id": "M2" }, { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/#F3", "location": "Fig3a–c caption; Results and Discussion", "note": "真实PSM成像、20min exposure、4×4binning、15h。", "checked": "2026-11-09", "id": "M3" }, { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/#F5", "location": "Mathematical Modeling", "note": "Fig5和Fig8是模拟。", "checked": "2026-11-09", "id": "M4" }, { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/", "location": "Image Analysis", "note": "ROI追踪/背景扣除与Excel存在声明。", "checked": "2026-11-09", "id": "M5" }, { "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/", "location": "Associated Data / Supplementary Materials", "note": "PMC列出三个MOV；其中Movie 2已下载和解码，见M8；其余视频未解码。", "checked": "2026-11-09", "id": "M6" }, { "id": "M7", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/", "location": "Materials and Methods · Bioluminescence Imaging of the PSM", "note": "浏览器正文核实：E10.5 PSM离体成像，37°C、5% CO₂、85% O₂；4×4 binning和20 min曝光。", "checked": "2026-11-09" }, { "id": "M8", "url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/1360553/bin/pnas_0508658103_08658Movie2.mov", "location": "Movie 2 · 本地下载和逐帧解码", "note": "实测2952078 bytes；45帧256×256灰度。SHA-256 455cdd3e3049351a064879e09ebcfa8ebd8be73d3d357eeb12bd42490465ce92。固定ROI及归一化参数见本地provenance.json。", "checked": "2026-11-09" } ], "assets": [ { "level": "figure", "level_label": "论文图", "label": "论文图", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/#F3", "format": "HTML figure", "bytes": null, "size": null, "status": "verified_article", "original_status": "verified_article_text", "evidence": "web搜索可读到完整Fig3 caption和正文；直接网页打开出现CAPTCHA。", "license": "Copyright © 2006 National Academy of Sciences; freely available via PNAS open access option", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie 2 (PSM; Fig3a)", "url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/1360553/bin/pnas_0508658103_08658Movie2.mov", "format": "MOV", "bytes": 2952078, "size": null, "status": "verified_content", "evidence": "已下载并完整解码45帧256×256灰度；官方补充视频，不等同于原始相机栈。", "license": "Copyright © 2006 National Academy of Sciences; freely available via PNAS open access option", "checked": "2026-11-09", "source_is_input": true }, { "level": "document", "level_label": "补充文档", "label": "补充文档", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/bin/pnas_0508658103_index.html", "format": "HTML index; PDF", "bytes": null, "size": "PMC列index3.7KB、PDF71.1/48.1/50.3KB；均为站点标注，非本次下载实测。", "status": "restricted", "original_status": "blocked", "evidence": "Supporting Information索引访问失败。", "license": "Copyright © 2006 National Academy of Sciences; freely available via PNAS open access option", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "强度 / kymograph 矩阵", "label": "强度 / kymograph 矩阵", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "not_found", "evidence": "Image Analysis说Excel记录ROI强度；未核实公开的Excel/矩阵入口。", "license": "Copyright © 2006 National Academy of Sciences; freely available via PNAS open access option", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "原始 time-lapse", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "not_found", "evidence": "未找到独立raw imaging仓库；补充movie不能等同原始曝光栈。", "license": "Copyright © 2006 National Academy of Sciences; freely available via PNAS open access option", "checked": "2026-11-09" }, { "level": "contact", "level_label": "需要联系作者", "label": "需要联系作者", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC1345707/", "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "possible_next_step_not_statement", "evidence": "若要ROI Excel、空间标定或原始栈，可能需要联系作者；本次未联系，原文未核实明确分享承诺。", "license": "Copyright © 2006 National Academy of Sciences; freely available via PNAS open access option", "checked": "2026-11-09" }, { "level": "derived", "level_label": "本地提取矩阵", "label": "Movie 2 · 160 × 45时空矩阵", "url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/1360553/bin/pnas_0508658103_08658Movie2.mov", "local_path": "data/derived/masamizu-2006/kymograph.npz", "format": "NPZ", "bytes": 46297, "status": "verified_content", "evidence": "逐帧取固定35 px条带并沿宽度平均。保存8-bit显示强度、统一归一化矩阵及帧/像素坐标；无时间平滑。", "license": "源视频版权归National Academy of Sciences；本地研究派生数据，未核实开放再利用许可。", "checked": "2026-11-09" } ], "recommendation": "可用于定性时空图比较；补齐时间、空间标定及组织运动校正后，再进行波速等定量比较。", "priority": 8, "verification_scope": "Movie 2 已下载并解码：45帧、256×256、8-bit灰度。正文核实37°C及20 min曝光；精确帧间隔、µm/px和原始相机栈仍未核实。", "field_evidence": { "species": [ "M1", "M2" ], "system_description": [ "M1", "M2" ], "tissue": [ "M1", "M2" ], "conditions": [ "M7" ], "reporter_construct": [ "M1", "M2" ], "reported_target": [ "M1", "M2" ], "time_axis": [ "M3" ], "space_axis": [ "M3" ], "time_resolution": [ "M3", "M8" ], "space_resolution": [ "M3", "M8" ], "replicates": [ "M3" ], "figure_focus": [ "M3", "M4" ], "preprocessing": [ "M5" ] }, "short": "Masamizu 2006", "reporter_short": "Hes1-Ub1-Luc", "reporter_tags": [ "Hes1-Ub1-Luc" ], "patterns": [ "振荡传播波", "形态学 somite boundaries", "单细胞振荡" ], "time_axis": "Fig3组织观察15 h，生物发光时序/ROI曲线；培养周期约160 min。", "space_axis": "caudal→rostral PSM / S0；绝对µm/pixel未知。", "time_resolution": "20 min是曝光时间；精确采样间隔未核实。", "space_resolution": "PSM成像4×4 binning；绝对空间采样未知。", "summary": "Hes1-Ub1-Luc 小鼠 PSM 的真实连续成像。已从 Movie 2 提取实验 kymograph，并保留取样区域与方法说明。", "calibration_short": "37°C · 45 帧 · 标定待补", "availability_status": "verified_content", "availability_summary": "45 帧已读取 · 已生成取样说明", "availability_filters": [ "论文图已核实", "补充视频已读取", "本地重绘已保存", "原始数值矩阵未定位" ], "caveats": [ "Fig5/8为数学模拟，不是实验kymograph。", "Hes1-Ub1-Luc报告promoter activity，非HES1蛋白绝对浓度。", "20 min exposure不等于已经核实的frame interval。", "培养周期约160 min，不能直接套用体内约120 min；fibroblast n=48不是PSM组织重复数。" ], "media": [], "checked": "2026-11-09", "kymograph": { "kind": "experimental", "short": "实验重绘 · 提取方法", "preview": null, "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/1360553/bin/pnas_0508658103_08658Movie2.mov", "note": "Movie 2 提取的160×45时空矩阵；固定35 px宽取样条。仅作定性预览，横轴为帧序号，纵轴为图像像素位置。" }, "compact_title": "Hes1 oscillations in mouse PSM", "method_figure": { "title": "实验重绘与取样说明", "preview": "figures/masamizu-2006/masamizu-movie2-kymograph.png", "alt": "Masamizu 2006：左侧为Movie 2实验首帧与橙色取样框，右侧为按帧排列的Hes1-Ub1-Luc实验kymograph。", "context": "Hes1-Ub1-Luc · 37°C · 45 帧", "summary": "这是一张取样方法说明图：左边标出实验视频中的取样区域，右边是从该区域提取的真实时空信号。", "steps": [ "在每帧的同一个35 px宽条带内取样，沿宽度求平均。", "把45帧的位置—强度曲线按时间排列，得到160×45的矩阵。", "整张矩阵统一归一化：浅色低、深色高；没有时间平滑。" ], "limit": "横轴是帧序号，纵轴是图像像素位置。时间及长度标尺尚未独立核实；组织生长和移动未校正，斜带的斜率不能直接当作波速。", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/1360553/bin/pnas_0508658103_08658Movie2.mov", "roi": "figures/masamizu-2006/roi-audit.png", "downloads": { "png": "figures/masamizu-2006/masamizu-movie2-kymograph.png", "svg": "figures/masamizu-2006/masamizu-movie2-kymograph.svg", "pdf": "figures/masamizu-2006/masamizu-movie2-kymograph.pdf" }, "data_path": "data/derived/masamizu-2006/kymograph.npz", "provenance_path": "data/derived/masamizu-2006/provenance.json" } }, { "id": "jiang-2000", "title": "Notch signalling and the synchronization of the somite segmentation clock", "authors": [ "Yun-Jin Jiang", "Birgit L. Aerne", "Lucy Smithers", "Catherine Haddon", "David Ish-Horowicz", "Julian Lewis" ], "year": 2000, "doi": "10.1038/35044091", "url": "https://www.nature.com/articles/35044091", "species": "Danio rerio", "tissue": "PSM; somite-stage embryos", "conditions": "WT and Notch-pathway mutants; live Bodipy-ceramide series at 10–13 somites, mounted laterally, 28–29°C", "reporter_construct": "无 live clock-gene reporter；supplementary movies use Bodipy-ceramide membrane vital dye", "reported_target": "Fixed deltaC / papc expression; live movies measure cell outlines and relative motion, not gene-expression oscillations", "figure_focus": "Fig.1–4 fixed deltaC/papc; Fig.5 is mechanism schematic. Movie 1a/b (Fig.S1) are cell motion only.", "time_axis": "Movies: 2 frames/min (30 s/frame); WT1a 60 min, aei1b 30 min", "space_axis": "anterior left; Movie Fig.S1 scale bar 30 µm; pixel size unknown", "replicates": "Supplement Table S1: WT 4 embryos (71,58,72,74 cells); bea 4 (71,72,71,76); aei 3 (72,57,70). Movies illustrate WT4 and aei3, not all replicates.", "caveats": [ "30 s time interval belongs to motion imaging and must not be used as clock reporter sampling.", "Full main-text access was restricted in web tool; publisher metadata/captions and public supplement DOC were read. No claim of complete full-text verification." ], "sources": [ { "id": "j-pubmed", "url": "https://pubmed.ncbi.nlm.nih.gov/11100729/", "location": "Metadata and abstract", "checked": "2026-11-09" }, { "id": "j-publisher", "url": "https://www.nature.com/articles/35044091", "location": "Publisher figure captions and Supplementary information; HTTP 200 HTML, main text purchase/access restriction", "checked": "2026-11-09" }, { "id": "j-supp", "url": "https://static-content.springer.com/esm/art%3A10.1038%2F35044091/MediaObjects/41586_2000_BF35044091_MOESM1_ESM.doc", "location": "Supplementary Information, Table S1, Figure S1 legends; HTTP 200, 25,600 bytes DOC, converted to text and read", "checked": "2026-11-09" }, { "id": "K1", "url": "https://www.nature.com/articles/35044091/figures/1", "location": "Figure 1 · deltaC 固定表达；实际Chrome网页", "note": "不同固定胚胎按表达相位排列；并非同一样本的连续时间帧。", "access": "图注及原图链接已核；未下载原始成像数据" } ], "field_evidence": { "species": [ "j-pubmed" ], "reporter_construct": [ "j-supp" ], "reported_target": [ "j-publisher" ], "sampling_interval_min": [ "j-supp" ], "time_axis": [ "j-supp" ], "space_axis": [ "j-supp" ], "replicates": [ "j-supp" ], "system_description": [], "time_resolution": [ "j-supp" ], "space_resolution": [ "j-supp" ], "kymograph": [ "K1" ] }, "recommendation": "用于 Notch synchronization 和配准/细胞运动背景；不要选作实验 clock kymograph 输入。", "species_label": "Zebrafish · 斑马鱼", "systems": [ "in vivo" ], "system_description": "in vivo; fixed expression assays plus live cell-motion microscopy", "assets": [ { "level": "document", "level_label": "补充文档", "label": "Supplementary information and movie legends", "url": "https://static-content.springer.com/esm/art%3A10.1038%2F35044091/MediaObjects/41586_2000_BF35044091_MOESM1_ESM.doc", "format": "DOC", "bytes": 25600, "size": null, "status": "verified_content", "original_status": "downloaded_and_read", "evidence": "HTTP 200; actual DOC signature/text converted and read", "license": "Nature publisher copyright; no open reuse license verified", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie 1a: WT cell movement (not clock reporter)", "url": "https://static-content.springer.com/esm/art%3A10.1038%2F35044091/MediaObjects/41586_2000_BF35044091_MOESM2_ESM.mov", "format": "MOV", "bytes": 1461920, "size": null, "status": "verified_headers", "original_status": "verified_headers", "evidence": "HEAD HTTP 200, application/octet-stream, Content-Length 1461920; film contents identified by supplementary legend, movie bytes not downloaded/played", "license": "Nature publisher copyright; no open reuse license verified", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "Movie 1b: aei cell movement (not clock reporter)", "url": "https://static-content.springer.com/esm/art%3A10.1038%2F35044091/MediaObjects/41586_2000_BF35044091_MOESM3_ESM.mov", "format": "MOV", "bytes": 1944592, "size": null, "status": "verified_headers", "original_status": "verified_headers", "evidence": "HEAD HTTP 200, application/octet-stream, Content-Length 1944592; film contents identified by supplementary legend, movie bytes not downloaded/played", "license": "Nature publisher copyright; no open reuse license verified", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "强度 / kymograph 矩阵", "label": "clock intensity/kymograph matrix", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "not_located", "evidence": "No public numerical expression matrix located in inspected metadata/supplement; main full text restricted.", "license": "unknown", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "clock-gene fluorescence raw imaging", "url": null, "format": null, "bytes": null, "size": null, "status": "not_applicable", "original_status": "not_applicable_to_verified_movies", "evidence": "Verified movie legends describe membrane dye cell tracking, not clock-gene reporter acquisition.", "license": "unknown", "checked": "2026-11-09" } ], "priority": 9, "short": "Jiang 2000", "journal": "Nature", "origin": "mixed", "origin_label": "固定表达 + 实时形态", "patterns": [ "固定表达条纹", "形态学 somite boundaries", "细胞运动" ], "reporter_short": "Bodipy-ceramide（膜染料）", "reporter_tags": [ "膜染料（非 clock reporter）", "ISH / FISH（非 live reporter）" ], "time_resolution": "运动视频30 s/frame；不能当clock gene采样。", "space_resolution": "视频标尺30 µm；µm/pixel未知。", "summary": "Notch 同步经典文献；可访问电影只显示细胞运动，不提供实时clock表达。", "calibration_short": "运动30 s · 标尺30 µm", "availability_status": "verified_headers", "availability_summary": "MOV 响应头可达 · 仅细胞运动", "availability_filters": [ "补充视频响应头已核", "数值矩阵未定位" ], "verification_scope": "metadata/摘要、出版社图注、公开补充DOC已读；全文访问受限；MOV仅核HEAD。", "preprocessing": "Bodipy膜边界追踪邻居位置；用于评估细胞运动和配准，不能替代基因表达强度。", "missing": [ "完整正文的未核细节", "视频像素尺度", "clock reporter实时信号不适用" ], "media": [ { "label": "Figure 1 · deltaC 固定表达", "url": "https://media.springernature.com/full/springer-static/image/art%3A10.1038%2F35044091/MediaObjects/41586_2000_Article_BF35044091_Fig1_HTML.jpg", "source_url": "https://www.nature.com/articles/35044091/figures/1", "description": "不同固定胚胎按表达相位排列；并非同一样本的连续时间帧。", "attribution": "Jiang et al. · Nature 408, 475–479 (2000) · DOI 10.1038/35044091 · © Nature / Springer Nature. 原来源加载。", "status": "2026-11-09已在实际Chrome原文页面核对图注和图片src；按需加载完整原图。" } ], "checked": "2026-11-09", "kymograph": { "kind": "fixed", "short": "固定样本 · 无实时 kymograph", "selector": "你截图中的固定样本", "order": 5, "preview": "https://media.springernature.com/full/springer-static/image/art%3A10.1038%2F35044091/MediaObjects/41586_2000_Article_BF35044091_Fig1_HTML.jpg", "source_url": "https://www.nature.com/articles/35044091/figures/1", "panel": "Fig. 1 · deltaC 表达快照", "panel_note": "不同固定胚胎按表达相位排列；并非同一样本的连续时间帧。", "attribution": "Jiang et al. · Nature 408, 475–479 (2000) · DOI 10.1038/35044091 · © Nature / Springer Nature. 原来源加载。", "focus": "表达相位的形态参考", "takeaway": "保留你选中的图。它展示 deltaC 的空间表达及相位类别，可与模型快照比较。", "reporter": "deltaC 原位表达 · 固定胚胎", "time": "无实测时间轴；I / II / III 为相位类别", "space": "胚胎后部；按脊索末端对齐", "signal": "原位杂交表达染色", "metrics": [ "空间表达", "相位类别" ], "limit": "不能据此生成真实时间 kymograph，也不能估计周期或波速。", "model_note": "可比较模型的相位快照与条纹位置。若需真实时间轨迹，请另看Soroldoni的斑马鱼实验：那是另一论文、另一reporter，并非本图对应样本。", "related": "soroldoni-2014" } }, { "id": "giudicelli-2007", "title": "Setting the Tempo in Development: An Investigation of the Zebrafish Somite Clock Mechanism", "authors": [ "François Giudicelli", "Ertuğrul M. Özbudak", "Gavin J. Wright", "Julian Lewis" ], "year": 2007, "doi": "10.1371/journal.pbio.0050150", "url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050150", "species": "Danio rerio", "tissue": "presomitic mesoderm (PSM)", "conditions": "7–15-somite fixed specimens for Fig.2; 28°C culture; 37°C heat-shock perturbations", "reporter_construct": "无动态荧光 clock reporter。hsp70:HA-her1 / hsp70:HA-her7 为诱导扰动构建；EF1alpha:GFP 是转基因识别标记。", "reported_target": "ISH/FISH: endogenous her1, her7, deltaC transcripts; zdc2 antibody: DeltaC protein", "figure_focus": "Fig.2A–C spatial profiles → inferred local period; Fig.4 nuclear/cytoplasmic intensity profiles. 不是实验 x(t,p) kymograph。", "time_axis": "Fig.2/4：由空间条纹、T0=30 min（28°C）与运动假设推断时间；Fig.8：恢复0、90、135、180 min后分别固定不同胚胎，非同一胚胎连续帧。", "space_axis": "A–P position x/L normalized to PSM length; wavelength in somite lengths", "replicates": "Fig.2: 10 embryos fixed at 7–15 somites; transcription-delay estimates: her1 n=10, her7 n=7, deltaC n=7", "caveats": [ "固定图空间–时间映射依赖稳态与细胞运动假设，不可当作 live time-lapse。", "ISH 染色强度不保证与 transcript 浓度严格线性。" ], "sources": [ { "id": "g-metadata", "url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050150", "location": "Citation; copyright; Results: The Temporal Sequence of Events...", "checked": "2026-11-09" }, { "id": "g-fig2", "url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050150#pbio-0050150-g002", "location": "Figure 2 caption; Eq.2", "checked": "2026-11-09" }, { "id": "g-methods", "url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050150", "location": "Materials and Methods: Generation of transgenic fish; Heat-shock procedures; Image analysis", "checked": "2026-11-09" }, { "id": "g-fig8", "url": "https://doi.org/10.1371/journal.pbio.0050150.g008", "location": "Figure 8 · 固定样本分时间点实验", "note": "恢复0、90、135、180 min后分别固定并做ISH；不是同一胚胎的连续成像。", "checked": "2026-11-09" }, { "id": "g-geo", "url": "https://www.ncbi.nlm.nih.gov/geoprofiles/?linkname=pmc_geoprofiles&from_uid=1877819", "location": "PMC → GEO Profiles · 全部关联记录", "note": "核对164条记录、21个数据集的标题与类型，均为表达芯片数据；未见本论文的连续成像数据集。", "checked": "2026-11-09" }, { "id": "g-geo-example", "url": "https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS5357", "location": "GDS5357 · 核对关联数据集的来源", "note": "关联列表首项为2014年胚胎眼睛酒精暴露研究，GSE51427，9个表达芯片样本；不是Giudicelli 2007。", "checked": "2026-11-09" } ], "field_evidence": { "species": [ "g-metadata" ], "system": [ "g-methods" ], "reporter_construct": [ "g-methods" ], "reported_target": [ "g-methods" ], "time_axis": [ "g-fig2", "g-fig8" ], "space_axis": [ "g-fig2" ], "replicates": [ "g-fig2" ], "system_description": [ "g-methods" ], "time_resolution": [ "g-fig8" ], "space_resolution": [ "g-fig2" ], "availability_summary": [ "g-methods", "g-geo", "g-geo-example" ] }, "recommendation": "机制/延迟约束参考；不作为重画 live kymograph 的首选。", "species_label": "Zebrafish · 斑马鱼", "systems": [ "in vivo" ], "system_description": "in vivo perturbation; fixed whole-mount ISH/FISH and confocal sections", "assets": [ { "level": "figure", "level_label": "论文图", "label": "Fig.2: fixed specimen and inferred period", "url": "https://journals.plos.org/plosbiology/article/figure/image?size=large&id=10.1371/journal.pbio.0050150.g002", "format": "PNG", "bytes": 1489861, "size": null, "status": "verified_headers", "original_status": "verified_headers", "evidence": "HEAD 200 image/png; web click cache miss; image bytes not downloaded", "license": "Creative Commons Attribution; article does not specify version in visible copyright statement", "checked": "2026-11-09" }, { "level": "figure", "level_label": "论文图", "label": "Fig.4: ISH intensity profiles", "url": "https://journals.plos.org/plosbiology/article/figure/image?size=large&id=10.1371/journal.pbio.0050150.g004", "format": "PNG", "bytes": 1568332, "size": null, "status": "verified_headers", "original_status": "verified_headers", "evidence": "HEAD 200 image/png", "license": "Creative Commons Attribution; see article copyright", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "强度 / kymograph 矩阵", "label": "数值强度矩阵", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "not_located", "evidence": "核读文章及下载区域未发现公开矩阵入口；这不证明作者没有保存数据。", "license": "unknown", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "连续 time-lapse · 未找到公开数据", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "original_status": "not_located", "evidence": "已检查论文全文、附件入口、BioStudies/DataCite检索与GEO Profiles关联记录，未找到本研究的连续成像文件。文中存在固定样本的分时间点实验（如Fig.8），不等同活体连续成像；作者是否保存其他未公开数据未知。", "license": "unknown", "checked": "2026-11-09" } ], "priority": 9, "short": "Giudicelli 2007", "journal": "PLOS Biology", "origin": "fixed", "origin_label": "固定样本 / 伪时间推断", "patterns": [ "固定表达条纹", "形态学 somite boundaries", "传播波（间接推断）" ], "reporter_short": "ISH / FISH · her1 / her7 / deltaC", "reporter_tags": [ "ISH / FISH（非 live reporter）" ], "time_resolution": "连续成像采样间隔不适用；Fig.8为固定样本的离散时间点。", "space_resolution": "绝对 µm/pixel 未核实；图使用 x/L 和 somite lengths。", "summary": "固定样本的空间表达与分时间点实验；未找到可重绘 kymograph 的公开连续成像数据。", "calibration_short": "非 time-lapse · x/L", "availability_status": "unknown", "availability_summary": "未找到连续成像数据", "availability_filters": [ "论文图已核实", "数值矩阵未定位" ], "verification_scope": "已核正文、方法、图注及公开附件，检索BioStudies、DataCite与GEO关联记录；未找到本研究的公开连续成像数据。GEO Profiles的164条记录涉及21个其他研究的表达芯片数据集，不能视为本文的原始数据。未据此断言作者没有未公开数据。", "preprocessing": "固定ISH/FISH图像空间轮廓；时间映射依赖稳态、组织速度与PSM归一化。", "missing": [ "绝对像素尺度", "机器可读原始表达轮廓", "连续成像数据未找到公开入口" ], "media": [ { "label": "Figure 2 · 固定样本与推导曲线", "url": "https://journals.plos.org/plosbiology/article/figure/image?size=large&id=10.1371/journal.pbio.0050150.g002", "source_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050150#pbio-0050150-g002", "description": "固定胚胎的表达图与推导周期；不是实验time-lapse kymograph。", "attribution": "Giudicelli et al., PLOS Biology (2007), Fig. 2. Creative Commons Attribution（原文未显示版本）.", "status": "HEAD 200 image/png；图像字节未下载。" } ], "checked": "2026-11-09", "kymograph": { "kind": "fixed", "short": "固定样本 · 非实时 kymograph", "preview": null, "source_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050150", "note": "未找到公开连续成像数据。Fig.2/4为固定样本的空间分布与时间推断；Fig.8有分时间点实验，但不是同一胚胎的time-lapse。" } }, { "id": "ilagan-2011", "short": "Ilagan 2011", "title": "Real-Time Imaging of Notch Activation with a Luciferase Complementation-Based Reporter", "authors": [ "Ma. Xenia G. Ilagan", "Sora Lim", "Mary Fulbright", "David Piwnica-Worms", "Raphael Kopan" ], "year": 2011, "journal": "Science Signaling", "doi": "10.1126/scisignal.2001656", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/", "species": "Homo sapiens / Mus musculus / Cricetulus griseus cell lines", "species_label": "Human / mouse / hamster · 培养细胞", "systems": [ "in vitro" ], "system_description": "3T3、OT11(RBPjκ−/−)、293T、HeLaTetON及CHO衍生细胞系；包含配体呈递细胞共培养。无胚胎或PSM组织实验。", "tissue": "不适用：培养细胞与孔板assay", "conditions": "37°C、5%CO₂；稳定HeLaTetON以0.5µg/ml doxycycline诱导。分别测Ca²⁺ chelator、γ-secretase inhibitor、CHX或Dll1/Jag1配体刺激；不是统一培养时序。", "origin": "live", "origin_label": "活细胞发光动力学 · 非体节", "reporter_short": "Notch-LCI · NICD–RBPjκ", "reporter_tags": [ "Notch-LCI", "split firefly luciferase" ], "reporter_construct": "mouse Notch1变体C端融合NLuc，配对CLuc–human RBPjκ(CSL)，含柔性Gly-Ser linker。变体含NotchFL、NLNG、NΔE、NICD；稳定株用Tet-inducible pBI双表达载体。NLuc指firefly luciferase片段，不是NanoLuc。", "reported_target": "NICD与CSL/RBPjκ蛋白结合使酶活互补，反映Notch受体激活/复合体量；并非Lfng/Hes时钟转录。Hes1/5-Luc与TP1-Luc用于独立endpoint验证；Fig8 LFNG为调节酶。", "patterns": [ "配体或药物响应", "复合体稳定性", "细胞核定位" ], "figure_focus": "Fig1示意；2–3构建与互作验证；4B为核定位图；5为降解动力学；6为γ-secretase抑制/恢复；7为EGTA激活；8为Dll1/Jag1响应。主图无组织kymograph。", "time_axis": "动力学曲线横轴为处理后时间，单位按图为min或h；不是胚胎分节时间轴。", "space_axis": "无组织位置轴；孔板ROI光子通量或细胞定位，不构成p×t矩阵。", "time_resolution": "Ca²⁺ chelator序列：每5min，共1h。其他动力学间隔未统一说明；IVIS曝光1–5min不能等同采样间隔。", "space_resolution": "未报告适合组织p轴的µm/pixel。Fig4B使用10×；IVIS视野12/15cm为孔板视野。", "replicates": "endpoint转录assay为quadruplicate；各动力学实验独立生物n未统一明确，不沿用该数。", "calibration_short": "5min仅限EGTA类序列 · 无组织p轴", "preprocessing": "ROI photon flux(photons/s)，报告mean±SD或对实验对照归一化；LivingImage2.6 / IGOR。Fig4定位图以ImageJ调亮度/对比度及despeckle，不是原始定量图。", "summary": "Notch蛋白互作的实时测量方法；没有体节时钟波形或组织kymograph。", "priority": 9, "recommendation": "保留为观测模型/报告器动力学参考；不作为poster x(p,t)或GFlowNet体节分割目标数据。", "availability_status": "restricted", "availability_summary": "全文已核 · 无体节kymograph · 补充DOCX受限", "availability_filters": [ "论文正文已核实", "非体节时空数据", "补充文件受限" ], "verification_scope": "完整PMC XML、Methods与8个主图caption已核；补充文件仅读取1KB响应，返回HTML而非DOCX。标题/DOI有限检索未定位raw或数值仓库；不声称全面排除未读补图。", "missing": [ "补充S1–S13内容未验证", "动力学曲线数值文件与原始发光图未定位", "主要动力学独立生物n未统一说明", "没有已核实的组织位置–时间数据" ], "caveats": [ "real-time Notch activation不等于segmentation-clock oscillations。", "NLuc/CLuc为酶片段互补，Hes转录reporter只是独立验证；不可混称Hes/Lfng clock数据。", "约180min是特定处理下复合体信号半衰期，不是振荡周期。", "主文全图审查支持无体节kymograph；受限补充文件尚未逐页核实。" ], "sources": [ { "id": "I1", "url": "https://pubmed.ncbi.nlm.nih.gov/21775282/", "location": "Bibliographic record", "note": "最终标题、5位作者、Sci Signal. 2011 Jul12;4(181):rs7；PMID21775282 / DOI10.1126/scisignal.2001656。", "checked": "2026-11-09" }, { "id": "I2", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#S3", "location": "Results: Robust and specific complementation; Figs1C/2A", "note": "Notch1-NLuc与CLuc-RBPjκ互补；短Gly-Ser linker；变体及对照。", "checked": "2026-11-09" }, { "id": "I3", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#S10", "location": "Materials and Methods: DNA constructs", "note": "mouse Notch1和human RBPjκ构建；Tet-inducible pBI dual vector；Hes1/5、TP1为另行转录reporter。", "checked": "2026-11-09" }, { "id": "I4", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#S11", "location": "Materials and Methods: Cell lines, Cell culture and plasmid transfections", "note": "3T3、OT11、293T、HeLaTetON及CHO细胞；37°C、5%CO₂及不同培养基。", "checked": "2026-11-09" }, { "id": "I5", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#S15", "location": "Materials and Methods: Bioluminescence Assays", "note": "Ca²⁺ chelator序列每5min持续1h；IVIS曝光1–5min；ROI photon flux和对照归一化。其他序列未统一声明采样间隔。", "checked": "2026-11-09" }, { "id": "I6", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#S16", "location": "Materials and Methods: Cellular bioluminescence imaging; Fig4", "note": "10×显微镜；Notch-LCI曝光5–10min，GL3对照30s–1min；核定位图而非kymograph。", "checked": "2026-11-09" }, { "id": "I7", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#S17", "location": "Materials and Methods: Transcriptional Reporter Assays", "note": "endpoint转录reporter为quadruplicate、48h取样；不能作为所有动力学的独立生物重复数。", "checked": "2026-11-09" }, { "id": "I8", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#F5", "location": "Figures5–8 captions; Results S4–S7", "note": "复合体稳定性、γ-secretase抑制/恢复、EGTA与ligand激活动力学；Fig5约180min为信号半衰期，不是时钟周期。", "checked": "2026-11-09" }, { "id": "I9", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#SM", "location": "Supplementary Material / Associated Data", "note": "仅列Supp Figs S1–S13，DOCX页面标称18.5MB；未列视频或原始成像/数值仓库。", "checked": "2026-11-09" }, { "id": "I10", "url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/3387985/bin/NIHMS360675-supplement-Supp_Figs_S1-S13.docx", "location": "2026-11-09 bounded Range GET", "note": "实际HTTP200 text/html，前1024bytes为HTML challenge，并非DOCX；没有下载或阅读补充正文。", "checked": "2026-11-09" }, { "id": "I11", "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=3387985&retmode=xml", "location": "NCBI PMC fulltext XML / permissions / main body and figure captions", "note": "已获取完整XML144777bytes；正文与Figs1–8核查无体节/PSM/kymograph。作者稿标题用using，最终PubMed标题用with。", "checked": "2026-11-09" }, { "id": "I12", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC514471/", "location": "Luker et al. 2004 abstract; Ilagan ref17 / Methods constructs", "note": "原始LCI方法使用firefly luciferase N/C-terminal fragments；本文NLuc不是NanoLuc。", "checked": "2026-11-09" } ], "field_evidence": { "title": [ "I1", "I11" ], "authors": [ "I1" ], "year": [ "I1" ], "journal": [ "I1" ], "doi": [ "I1" ], "species": [ "I3", "I4" ], "system_description": [ "I4" ], "tissue": [ "I4", "I11" ], "conditions": [ "I4", "I5" ], "origin": [ "I5", "I6" ], "reporter_construct": [ "I2", "I3", "I12" ], "reported_target": [ "I2", "I3", "I8" ], "patterns": [ "I6", "I8" ], "figure_focus": [ "I2", "I6", "I8", "I11" ], "time_axis": [ "I5", "I8" ], "space_axis": [ "I5", "I6", "I11" ], "time_resolution": [ "I5" ], "space_resolution": [ "I5", "I6" ], "replicates": [ "I7", "I11" ], "preprocessing": [ "I5", "I6" ], "recommendation": [ "I2", "I5", "I11" ], "availability_summary": [ "I9", "I10", "I11" ], "kymograph": [ "I6", "I8", "I11" ] }, "assets": [ { "level": "figure", "level_label": "论文图", "label": "Figs1–8 · Notch方法/实验曲线", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/#F1", "format": "HTML / JATS", "bytes": null, "size": null, "status": "verified_article", "evidence": "完整XML及8个图注已核；未将定位图或曲线当作组织kymograph。", "license": "AAAS / Science Signaling 作者稿；PMC仅说明text mining及fair use，未核实CC或开放再利用许可。", "checked": "2026-11-09" }, { "level": "supplement", "level_label": "补充材料", "label": "Supp Figs S1–S13", "url": "https://pmc.ncbi.nlm.nih.gov/articles/instance/3387985/bin/NIHMS360675-supplement-Supp_Figs_S1-S13.docx", "format": "DOCX（页面列出）", "bytes": null, "size": "18.5 MB（PMC页面标注；未实测总文件大小）", "status": "restricted", "evidence": "实测仅返回HTML challenge；扩展名与页面大小不代表文件本体验证。", "license": "AAAS / Science Signaling 作者稿；PMC仅说明text mining及fair use，未核实CC或开放再利用许可。", "checked": "2026-11-09" }, { "level": "movie", "level_label": "补充视频", "label": "未定位公开视频入口", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "evidence": "所查正文与Associated Data未列movie；未读补充文件，不能断言不存在。", "license": "未知", "checked": "2026-11-09" }, { "level": "matrix", "level_label": "强度 / kymograph 矩阵", "label": "未定位数值数据；无已核体节矩阵", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "evidence": "主文为Notch动力学曲线；标题/DOI及关联数据检索未定位可验证数字矩阵。", "license": "未知", "checked": "2026-11-09" }, { "level": "raw", "level_label": "原始 time-lapse", "label": "原始发光序列", "url": null, "format": null, "bytes": null, "size": null, "status": "unknown", "evidence": "正文描述serial imaging，但未定位原始图像仓库；不把论文图当raw。", "license": "未知", "checked": "2026-11-09" } ], "media": [], "checked": "2026-11-09", "kymograph": { "kind": "traces", "short": "Notch方法 · 无体节kymograph", "preview": null, "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3387985/", "note": "主文为NICD–RBPjκ互补发光曲线及细胞定位，缺少组织位置轴；不展示为poster的实验时空图。" }, "pmid": "21775282", "pmcid": "PMC3387985", "volume": "4", "issue": "181", "article_number": "rs7", "publication_date": "2011-07-12", "origin_badge": "Notch 方法" }, { "id": "rohde-2024", "short": "Rohde 2024", "title": "Cell-autonomous timing drives the vertebrate segmentation clock’s wave pattern", "authors": [ "Laurel A Rohde", "Arianne Bercowsky-Rama", "Guillaume Valentin", "Sundar Ram Naganathan", "Ravi A Desai", "Petr Strnad", "Daniele Soroldoni", "Andrew C Oates" ], "year": 2024, "doi": "10.7554/eLife.93764", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11643631/", "species": "Danio rerio", "species_label": "Zebrafish · 斑马鱼", "systems": [ "in vivo" ], "system_description": "活体斑马鱼光片成像与Mastodon细胞追踪", "tissue": "Tailbud / PSM / somites", "conditions": "28.5°C；活体光片成像", "reporter_construct": "Tg(her1:her1-YFP); Tg(h2b-mCherry) nuclear marker; looping line", "reported_target": "Her1-YFP fusion fluorescence, mean intensity within 3-D segmented cell/nuclear spot; her1 reporter protein, not direct transcript abundance", "reporter_tags": [ "Her1–YFP" ], "origin": "live", "origin_label": "真实 time-lapse", "patterns": [ "振荡传播波" ], "time_axis": "h", "space_axis": "按所用样本标定", "time_resolution": "90 s/stack；不使用影片播放帧率", "space_resolution": "xy 0.347 µm；z层距1.5 µm；细胞轨迹坐标以µm存储", "replicates": "本轮仅选择一个代表记录，不作为生物学重复统计", "figure_focus": "Fig.1细胞强度；Fig.2末次峰值及Mesp onset事件图，不能直接作为连续强度矩阵", "preprocessing": "从作者CSV取Mean ch0（Her1-YFP）与XYZ，逆转逐帧affine配准，按当帧脊索ROI投影。每20µm、每90s取实测spot算术平均；保留cell_count和NaN。16×300矩阵中实测位于0.25–5.50h，未插值、补洞或平滑。颜色仅按完整矩阵的有限值归一化。", "sources": [ { "id": "S1", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/In_vivo_data/Position2_TB_to_TB_PSM_SOM-vertices.csv", "location": "vertices.csv", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S2", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/In_vivo_data/Position2_TB_to_TB_PSM_SOM-edges.csv", "location": "edges.csv", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S3", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/In_vivo_data/Position2_20191213.xml", "location": "acquisition.xml", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S4", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/In_vivo_data/RoiSet-Position2.zip", "location": "RoiSet.zip", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S5", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/utils/MastodonFunctions.py", "location": "MastodonFunctions.py", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S6", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/README.md", "location": "README.md", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S7", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/LICENSE", "location": "LICENSE", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S8", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/notebooks/TB_dynamics_in_embryo.ipynb", "location": "notebook.ipynb", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S9", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/Figure%202/Figure%202%20-%20In%20vivo/Position2-vertices.csv", "location": "psm-vertices.csv", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S10", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/Figure%202/Figure%202%20-%20In%20vivo/Position2-edges.csv", "location": "psm-edges.csv", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S11", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/In_vivo_data/Tiffs/Time150min.tif", "location": "Time150min.tif", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S12", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/In_vivo_data/Tiffs/Time300min.tif", "location": "Time300min.tif", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S13", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/notebooks/PSM4_Dynamics_in_the_embryo_Part_I.ipynb", "location": "psm-notebook.ipynb", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S14", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/Figure%202/Figure%202%20-%20In%20vivo/Position2-20191213-PSMd-vertices.csv", "location": "psm4-vertices.csv", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S15", "url": "https://raw.githubusercontent.com/EPFL-TOP/WSC_NotebooksPaper/f09fa8ca5a798e1991130d3c9225e8e82ff60317/Data/Figure%202/Figure%202%20-%20In%20vivo/Position2-20191213-PSMd-edges.csv", "location": "psm4-edges.csv", "note": "实际文件已读取，SHA256见完整记录。" }, { "id": "S16", "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=11643631&retmode=xml", "location": "article.xml", "note": "实际文件已读取，SHA256见完整记录。" } ], "field_evidence": { "conditions": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16" ], "reporter_construct": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16" ], "time_resolution": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16" ], "space_axis": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16" ], "preprocessing": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16" ], "figure_focus": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16" ] }, "assets": [ { "level": "matrix", "level_label": "本地重绘矩阵", "label": "轨迹分箱", "url": "https://github.com/EPFL-TOP/WSC_NotebooksPaper", "format": "NPZ", "bytes": 692859, "status": "verified_content", "evidence": "实测细胞强度已分箱重绘；仅PSM4细胞队列，空格无测量；覆盖边缘不是组织生长前沿。", "license": "Apache 2.0（代码仓库根许可，未见单独数据许可）；论文CC BY 4.0；保留作者署名", "local_path": "data/derived/rohde-2024/psm4_cohort.npz" }, { "level": "document", "level_label": "处理记录", "label": "来源、参数与限制", "url": "https://github.com/EPFL-TOP/WSC_NotebooksPaper", "format": "JSON", "bytes": null, "status": "verified_content", "evidence": "从作者CSV取Mean ch0（Her1-YFP）与XYZ，逆转逐帧affine配准，按当帧脊索ROI投影。每20µm、每90s取实测spot算术平均；保留cell_count和NaN。16×300矩阵中实测位于0.25–5.50h，未插值、补洞或平滑。颜色仅按完整矩阵的有限值归一化。", "license": "本地分析记录", "local_path": "data/derived/rohde-2024/provenance.json" }, { "level": "matrix", "level_label": "另一独立队列", "label": "Tailbud cohort · NPZ", "url": "https://github.com/EPFL-TOP/WSC_NotebooksPaper", "format": "NPZ", "bytes": 573902, "status": "verified_content", "evidence": "另一独立导出队列；不与PSM4拼接。实测0.25–7.45h；保留count与NaN。", "license": "Apache 2.0（代码仓库根许可，未见单独数据许可）；论文CC BY 4.0；保留作者署名", "local_path": "data/derived/rohde-2024/tailbud_cohort.npz" } ], "media": [], "missing": [ "这是公开连续强度轨迹分箱重绘，不是作者Fig.2 last-peak/onset事件图，也不是原始全组织像素kymograph。", "每个矩阵只覆盖一个选定细胞队列。斜向覆盖边界包含细胞前向流动及取样范围，不能把它当作传播波速。未测量处不能解释为Her1=0。", "source CSV本身已由作者3-D分割并Gaussian-filter处理；这里没有从原始H5重新测量。", "保留每个export的全部spot；45和101是track-ID数，不强称独立非分裂细胞数或论文最终纳入n。", "由2-D notochord投影降维，不含组织厚度或横向结构。", "强度含背景和reporter成熟/降解，不等于模拟基因表达浓度，跨数据集不可直接比较绝对counts。", "TIFF是作者已渲染的8-bit RGB最大投影，仅作几何核对，不能用其RGB颜色回推定量荧光。150/300min与frame100/200相符；未使用notebook中存在命名/帧号偏差的0/450min示例。", "第一批跟踪点是15min；显示0–10h时必须保留开始和结束的NaN，不能延长数据或重定时。", "作者notebook用ROI浮点坐标强制转整数；本提取保留ROI的原始subpixel精度，以20分段同法投影。因此不声称逐像素精确复制作者旧图。" ], "checked": "2026-11-09", "recommendation": "先核实时间、空间与通道，再用于模型定性对照。", "summary": "以细胞追踪分析时钟减慢与波形；公开成像、细胞强度和坐标。", "caveats": [ "这是公开连续强度轨迹分箱重绘，不是作者Fig.2 last-peak/onset事件图，也不是原始全组织像素kymograph。", "每个矩阵只覆盖一个选定细胞队列。斜向覆盖边界包含细胞前向流动及取样范围，不能把它当作传播波速。未测量处不能解释为Her1=0。", "source CSV本身已由作者3-D分割并Gaussian-filter处理；这里没有从原始H5重新测量。", "保留每个export的全部spot；45和101是track-ID数，不强称独立非分裂细胞数或论文最终纳入n。", "由2-D notochord投影降维，不含组织厚度或横向结构。", "强度含背景和reporter成熟/降解，不等于模拟基因表达浓度，跨数据集不可直接比较绝对counts。", "TIFF是作者已渲染的8-bit RGB最大投影，仅作几何核对，不能用其RGB颜色回推定量荧光。150/300min与frame100/200相符；未使用notebook中存在命名/帧号偏差的0/450min示例。", "第一批跟踪点是15min；显示0–10h时必须保留开始和结束的NaN，不能延长数据或重定时。", "作者notebook用ROI浮点坐标强制转整数；本提取保留ROI的原始subpixel精度，以20分段同法投影。因此不声称逐像素精确复制作者旧图。" ], "priority": 1, "reporter_short": "Her1–YFP", "calibration_short": "90 s · 20 µm分箱", "availability_status": "verified_content", "availability_summary": "实测细胞强度已分箱重绘", "availability_filters": [ "数据已读取", "已重绘" ], "verification_scope": "实际数据文件已读取，来源、标定与缺口见处理记录。", "journal": "eLife", "compact_title": "Cell-autonomous wave timing", "kymograph": { "source_url": "https://github.com/EPFL-TOP/WSC_NotebooksPaper", "attribution": "数据：Rohde 2024；Clock Explorer 根据实际取得的数据重绘，非原论文面板。", "focus": "同一风格，保留数据边界", "takeaway": "实测细胞强度已分箱重绘", "reporter": "Her1–YFP", "time": "90 s/列；原始采集帧0为起点，实测0.25–5.50h", "space": "µm；距当帧后端脊索参考点的投影距离", "signal": "完整样本独立归一化 · 0–1", "metrics": [ "传播波", "时间尺度" ], "limit": "仅PSM4细胞队列，空格无测量；覆盖边缘不是组织生长前沿。", "model_note": "从作者CSV取Mean ch0（Her1-YFP）与XYZ，逆转逐帧affine配准，按当帧脊索ROI投影。每20µm、每90s取实测spot算术平均；保留cell_count和NaN。16×300矩阵中实测位于0.25–5.50h，未插值、补洞或平滑。颜色仅按完整矩阵的有限值归一化。", "panel_note": "仅PSM4细胞队列，空格无测量；覆盖边缘不是组织生长前沿。", "panel": "Rohde 2024 · Her1–YFP", "kind": "experimental", "short": "Kymograph · 数据重绘", "selector": "轨迹分箱", "order": 12, "no_original": true, "preview": "figures/comparison/rohde-2024-full.svg", "rendered": { "intensity": { "source_url": "https://github.com/EPFL-TOP/WSC_NotebooksPaper", "attribution": "数据：Rohde 2024；Clock Explorer 根据实际取得的数据重绘，非原论文面板。", "focus": "同一风格，保留数据边界", "takeaway": "实测细胞强度已分箱重绘", "reporter": "Her1–YFP", "time": "90 s/列；原始采集帧0为起点，实测0.25–5.50h", "space": "µm；距当帧后端脊索参考点的投影距离", "signal": "完整样本独立归一化 · 0–1", "metrics": [ "传播波", "时间尺度" ], "limit": "仅PSM4细胞队列，空格无测量；覆盖边缘不是组织生长前沿。", "model_note": "从作者CSV取Mean ch0（Her1-YFP）与XYZ，逆转逐帧affine配准，按当帧脊索ROI投影。每20µm、每90s取实测spot算术平均；保留cell_count和NaN。16×300矩阵中实测位于0.25–5.50h，未插值、补洞或平滑。颜色仅按完整矩阵的有限值归一化。", "panel_note": "仅PSM4细胞队列，空格无测量；覆盖边缘不是组织生长前沿。", "panel": "Rohde 2024 · Her1–YFP", "preview": "figures/comparison/rohde-2024-full.svg", "downloads": { "svg": "figures/comparison/rohde-2024-full.svg", "pdf": "figures/comparison/rohde-2024-full.pdf", "png": "figures/comparison/rohde-2024-full.png" } } }, "card_context": { "condition": "28.5°C", "sample": "PSM4 · Position 2", "source_url": "https://elifesciences.org/articles/93764#s4", "evidence": "活体光片成像Methods；跟踪样本20191213 Position2。" }, "comparison": { "short": "Rohde 2024", "reporter": "Her1–YFP", "kind": "tracks", "source_label": "轨迹分箱", "label": "Tracked cells · 20 µm bins", "source_url": "https://github.com/EPFL-TOP/WSC_NotebooksPaper", "position_unit": "µm", "origin": "each frame's first notochord ROI point, identified as posterior tail-tip reference in author notebook", "origin_short": "细胞队列 · 20 µm", "sample": "PSM4 · Position 2", "roi": "figures/rohde-2024/roi-overlay.png", "coverage_note": "实测 0.25–5.50 h · 211 帧", "roi_note": "150与300min的公开投影图、作者脊索ROI及逆变换后的细胞位置。强度来自CSV；RGB图只用于检查取样几何。", "id": "rohde-2024", "provenance": "data/derived/rohde-2024/provenance.json", "input": "data/derived/rohde-2024/psm4_cohort.npz", "input_sha256": "c91153649cab01f2627235f7d87cafdd960136e5281596ddedefe46f4f5d7617", "shape_space_time": [ 16, 300 ], "time_range_h": [ 0.0, 7.475 ], "spatial_range": [ 10.0, 310.0 ], "missing_values": 3626, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 115.522137771044, "max": 426.423828843253 }, "spatial_range_um": [ 10.0, 310.0 ], "common_preview": "figures/comparison/rohde-2024-common.svg", "full_preview": "figures/comparison/rohde-2024-full.svg" } } }, { "id": "sanaki-2022", "short": "Sanaki-Matsumiya 2022", "title": "Periodic formation of epithelial somites from human pluripotent stem cells", "authors": [ "Marina Sanaki-Matsumiya", "Mitsuhiro Matsuda", "Nicola Gritti", "Fumio Nakaki", "James Sharpe", "Vikas Trivedi", "Miki Ebisuya" ], "year": 2022, "doi": "10.1038/s41467-022-29967-1", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/", "species": "Homo sapiens", "species_label": "Human · 人", "systems": [ "in vitro" ], "system_description": "人iPSC来源三维somitoid", "tissue": "PSM / somitoid", "conditions": "day4开始；N2B27 + 0.5mM luciferin + 10% Matrigel。LV200影片温度未单独注明。", "reporter_construct": "HES7–luciferase", "reported_target": "报告基因表达相关信号；不等于绝对分子浓度", "reporter_tags": [ "HES7–luciferase" ], "origin": "live", "origin_label": "真实 time-lapse", "patterns": [ "振荡传播波" ], "time_axis": "h", "space_axis": "按所用样本标定", "time_resolution": "Methods：5或10 min/frame；具体影片以帧内时间核对。", "space_resolution": "未确认", "replicates": "本轮仅选择一个代表记录，不作为生物学重复统计", "figure_focus": "Fig.3c的AP kymograph；Supplementary Movie4", "preprocessing": "明场分割得到每帧质心和主轴，以2个视频像素分箱；将同步reporter面板的RGB近似映射到ImageJ Fire色阶。 RGB色差>30的像素剔除，空格保留NaN。此阈值是本地分析规则，不是作者数据质量标准。亮部选择性剔除会造成偏差，不用于振幅、细胞或波速定量。", "sources": [ { "id": "S1", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9050736.1/41467_2022_29967_MOESM9_ESM.mp4", "location": "movie4.mp4", "note": "Downloaded successfully from the public official endpoint; opened locally." }, { "id": "S2", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9050736.1/41467_2022_29967_MOESM12_ESM.xlsx", "location": "source-data.xlsx", "note": "Downloaded successfully from the public official endpoint; opened locally." }, { "id": "S3", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9050736.1/41467_2022_29967_MOESM2_ESM.pdf", "location": "supplement-captions.pdf", "note": "Downloaded successfully from the public official endpoint; opened locally." }, { "id": "S4", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9050736.1/PMC9050736.1.xml", "location": "article.xml", "note": "Downloaded and opened; official public endpoint." }, { "id": "S5", "url": "https://raw.githubusercontent.com/imagej/imagej-common/main/src/main/resources/luts/Fire.lut", "location": "fire.lut", "note": "Downloaded and opened; official public endpoint." }, { "id": "S6", "url": "https://raw.githubusercontent.com/imagej/imagej-common/main/LICENSE.txt", "location": "IMAGEJ-LICENSE.txt", "note": "Downloaded and opened; official public endpoint." }, { "id": "S7", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9050736.1/41467_2022_29967_Fig3_HTML.jpg", "location": "figure3.jpg", "note": "Downloaded and opened; official public endpoint." }, { "id": "S8", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/#Fig3", "location": "Methods / figure / video caption", "note": "Fig3a/b identify the HES7 reporter and Movie4; c is posterior-anterior kymograph; d notes halts for repositioning." }, { "id": "S9", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/#Sec20", "location": "Par39", "note": "Day4, lipidure dish, 0.5mM luciferin, 10% Matrigel, LV200 10x, 5/10min sampling, 100ms bright-field and1.5min luminescent exposure." }, { "id": "S10", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/#Sec20", "location": "Par40", "note": "Authors used median filtering, tissue alignment and reslicing. Our method is separately documented and does not claim exact author processing." } ], "field_evidence": { "conditions": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "reporter_construct": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "time_resolution": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "space_axis": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "preprocessing": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "figure_focus": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ] }, "assets": [ { "level": "matrix", "level_label": "本地重绘矩阵", "label": "视频色阶近似", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/", "format": "NPZ", "bytes": 56856, "status": "verified_content", "evidence": "视频色阶近似 · 仅定性；前99帧；未标定µm；约11.2%组织像素因色差被排除。", "license": "CC BY 4.0；ImageJ LUT: BSD 2-Clause", "local_path": "data/derived/sanaki-2022/kymograph.npz" }, { "level": "document", "level_label": "处理记录", "label": "来源、参数与限制", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/", "format": "JSON", "bytes": null, "status": "verified_content", "evidence": "明场分割得到每帧质心和主轴，以2个视频像素分箱；将同步reporter面板的RGB近似映射到ImageJ Fire色阶。 RGB色差>30的像素剔除，空格保留NaN。此阈值是本地分析规则，不是作者数据质量标准。亮部选择性剔除会造成偏差，不用于振幅、细胞或波速定量。", "license": "本地分析记录", "local_path": "data/derived/sanaki-2022/provenance.json" }, { "level": "movie", "level_label": "原始附件视频", "label": "Movie 4", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC9050736.1/41467_2022_29967_MOESM9_ESM.mp4", "format": "MP4", "bytes": 12938453, "status": "verified_content", "evidence": "已完整解码。对比只采用连续早期窗口；原视频未随交付包分发。", "license": "CC BY 4.0；ImageJ LUT: BSD 2-Clause" } ], "media": [], "missing": [ "仅前99帧连续区间，不补后续调整样本造成的间隙。", "Fire LUT为与官方标准色轨迹匹配的推断，作者未提供精确LUT。", "约11.2%组织像素被残差规则排除；亮像素的排除可能影响振幅。", "组织外部及不足3个有效像素的bin为NaN，并非零表达。", "主轴投影不追踪同一细胞，也不消除弯曲。", "LV200实际成像温度未单独注明。" ], "checked": "2026-11-09", "recommendation": "先核实时间、空间与通道，再用于模型定性对照。", "summary": "人源somitoid中HES7振荡与传播波，可与体节形成对照。", "caveats": [ "仅前99帧连续区间，不补后续调整样本造成的间隙。", "Fire LUT为与官方标准色轨迹匹配的推断，作者未提供精确LUT。", "约11.2%组织像素被残差规则排除；亮像素的排除可能影响振幅。", "组织外部及不足3个有效像素的bin为NaN，并非零表达。", "主轴投影不追踪同一细胞，也不消除弯曲。", "LV200实际成像温度未单独注明。" ], "priority": 1, "reporter_short": "HES7–luciferase", "calibration_short": "10 min · 视频像素", "availability_status": "verified_content", "availability_summary": "视频色阶近似 · 仅定性", "availability_filters": [ "数据已读取", "已重绘" ], "verification_scope": "实际数据文件已读取，来源、标定与缺口见处理记录。", "journal": "Nature Communications", "compact_title": "Human somitoid oscillations", "kymograph": { "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/", "attribution": "数据：Sanaki-Matsumiya 2022；Clock Explorer 根据实际取得的数据重绘，非原论文面板。", "focus": "同一风格，保留数据边界", "takeaway": "视频色阶近似 · 仅定性", "reporter": "HES7 promoter–luciferase", "time": "10 min/帧；day4成像起点为0", "space": "逐帧质心为0的主轴视频像素", "signal": "相对色阶索引 · 非原始荧光强度", "metrics": [ "传播波", "时间尺度" ], "limit": "前99帧；未标定µm；约11.2%组织像素因色差被排除。", "model_note": "明场分割得到每帧质心和主轴，以2个视频像素分箱；将同步reporter面板的RGB近似映射到ImageJ Fire色阶。 RGB色差>30的像素剔除，空格保留NaN。此阈值是本地分析规则，不是作者数据质量标准。亮部选择性剔除会造成偏差，不用于振幅、细胞或波速定量。", "panel_note": "前99帧；未标定µm；约11.2%组织像素因色差被排除。", "panel": "Sanaki-Matsumiya 2022 · HES7–luciferase", "kind": "experimental", "short": "Kymograph · 数据重绘", "selector": "视频色阶近似", "order": 13, "no_original": true, "preview": "figures/comparison/sanaki-2022-full.svg", "rendered": { "intensity": { "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/", "attribution": "数据：Sanaki-Matsumiya 2022；Clock Explorer 根据实际取得的数据重绘，非原论文面板。", "focus": "同一风格，保留数据边界", "takeaway": "视频色阶近似 · 仅定性", "reporter": "HES7 promoter–luciferase", "time": "10 min/帧；day4成像起点为0", "space": "逐帧质心为0的主轴视频像素", "signal": "相对色阶索引 · 非原始荧光强度", "metrics": [ "传播波", "时间尺度" ], "limit": "前99帧；未标定µm；约11.2%组织像素因色差被排除。", "model_note": "明场分割得到每帧质心和主轴，以2个视频像素分箱；将同步reporter面板的RGB近似映射到ImageJ Fire色阶。 RGB色差>30的像素剔除，空格保留NaN。此阈值是本地分析规则，不是作者数据质量标准。亮部选择性剔除会造成偏差，不用于振幅、细胞或波速定量。", "panel_note": "前99帧；未标定µm；约11.2%组织像素因色差被排除。", "panel": "Sanaki-Matsumiya 2022 · HES7–luciferase", "preview": "figures/comparison/sanaki-2022-full.svg", "downloads": { "svg": "figures/comparison/sanaki-2022-full.svg", "pdf": "figures/comparison/sanaki-2022-full.pdf", "png": "figures/comparison/sanaki-2022-full.png" } } }, "card_context": { "condition": "温度未注明", "sample": "Movie 4 · day 4", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/#Sec20", "evidence": "Methods Par38 specifies 37 C and 5% CO2 for Opera Phenix bright-field time-lapse. Separate LV200 section Par39 gives no temperature. Do not transfer that set point to Movie 4. General iPSC culture in Par29 was also 37 C." }, "comparison": { "short": "Sanaki-Matsumiya 2022", "reporter": "HES7–luciferase", "kind": "video_lut", "source_label": "视频色阶近似", "label": "Approx. video color index", "signal_label": "Relative color index", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/", "roi": "figures/sanaki-2022/roi-overlay.png", "native_space_only": true, "position_unit": "video px", "origin": "Per-frame bright-field tissue centroid", "origin_short": "主轴 · 视频像素", "axis_label": "Axial position (video px)", "sample": "Movie 4 · day 4", "roi_note": "显示实际取样范围及高色差掩膜。仅近似恢复影片色阶；被排除的亮像素会影响强度解释。", "coverage_note": "连续段 99 帧 · 16.33 h", "id": "sanaki-2022", "provenance": "data/derived/sanaki-2022/provenance.json", "input": "data/derived/sanaki-2022/kymograph.npz", "input_sha256": "7ddb4dbd492917497bd818920b9461fa4af4194cba7e436cb17835fba361a63e", "shape_space_time": [ 120, 99 ], "time_range_h": [ 0.0, 16.333333333333332 ], "spatial_range": [ -119.0, 119.0 ], "missing_values": 5226, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 2.6666667461395264, "max": 246.19100952148438 }, "common_preview": "figures/comparison/sanaki-2022-common.svg", "full_preview": "figures/comparison/sanaki-2022-full.svg" } } }, { "id": "yaman-2023", "short": "Yaman 2023", "title": "Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves", "authors": [ "Yusuf Ilker Yaman", "Sharad Ramanathan" ], "year": 2023, "doi": "10.1016/j.cell.2022.12.042", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10025047/", "species": "Homo sapiens", "species_label": "Human · 人", "systems": [ "in vitro" ], "system_description": "NCRM1 iPSC来源人轴向类器官", "tissue": "PSM / somitoid", "conditions": "成像方法：37°C、5% CO₂；DGIP + 6% Matrigel。代码示例的具体处理组待确认。", "reporter_construct": "内源HES7-Achilles；MESP2-mCherry双报告系统", "reported_target": "报告基因表达相关信号；不等于绝对分子浓度", "reporter_tags": [ "HES7–Achilles" ], "origin": "live", "origin_label": "真实 time-lapse", "patterns": [ "振荡传播波" ], "time_axis": "h", "space_axis": "按所用样本标定", "time_resolution": "15 min/frame；作者脚本0.25 h/列", "space_resolution": "示例TIFF缺物理空间标定；保留存储行坐标，不将DPI当µm", "replicates": "本轮仅选择一个代表记录，不作为生物学重复统计", "figure_focus": "Fig.3C的HES7/MESP2 kymographs；MovieS2 control及扰动；代码附带示例Kymograph.tif", "preprocessing": "从论文链接的Zenodo v1.0代码包读取Phase_Calculation/Kymograph.tif，395×172 uint16。依作者脚本以0.25h/列标时间；未改值、翻转或平滑。比较图对完整矩阵min–max归一化。具体样本、通道、条件和绝对分化时间未知。", "sources": [ { "id": "S1", "url": "https://pubmed.ncbi.nlm.nih.gov/36657441/", "location": "Citation; metadata", "note": "Authors,2023,Cell186(3),513–527.e19,DOI." }, { "id": "S2", "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=10025047&retmode=xml", "location": "Cell lines; Time-lapse imaging of organoids; Analysis of time-lapse imaging data and generation of kymographs", "note": "NCRM1/reporters,37°C,15min acquisition,empirical image processing." }, { "id": "S3", "url": "https://zenodo.org/records/7458178", "location": "Software deposit,files and related_identifiers", "note": "Official paper-linked v1.0 archive,other-open license; archive downloaded and inspected." }, { "id": "S4", "url": "https://github.com/yilkeryaman/somiteOrganoids/tree/v1.0", "location": "README; Phase_Calculation/Kymograph.tif; phase_Calculation.m", "note": "README explicitly provides sample Kymograph; MATLAB reads each row as trace and sets dt=0.25h. Simulation in separate directory." }, { "id": "S5", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10025047/", "location": "Data and Code Availability; MovieS2 caption", "note": "Raw microscopy upon request; MovieS2A control72–138h but not linked to TIFF example." } ], "field_evidence": { "conditions": [ "S1", "S2", "S3", "S4", "S5" ], "reporter_construct": [ "S1", "S2", "S3", "S4", "S5" ], "time_resolution": [ "S1", "S2", "S3", "S4", "S5" ], "space_axis": [ "S1", "S2", "S3", "S4", "S5" ], "preprocessing": [ "S1", "S2", "S3", "S4", "S5" ], "figure_focus": [ "S1", "S2", "S3", "S4", "S5" ] }, "assets": [ { "level": "matrix", "level_label": "本地重绘矩阵", "label": "作者矩阵", "url": "https://zenodo.org/records/7458178", "format": "NPZ", "bytes": 80775, "status": "verified_content", "evidence": "作者示例矩阵已读取并重绘；示例通道与条件未标注；空间是行号，不是µm。", "license": "Zenodo access_right=open, license.id=other-open. No explicit license file in v1.0 archive; do not assume CC. Paper under Elsevier user license; local analytical use only, not uploaded.", "local_path": "data/derived/yaman-2023/kymograph.npz" }, { "level": "document", "level_label": "处理记录", "label": "来源、参数与限制", "url": "https://zenodo.org/records/7458178", "format": "JSON", "bytes": null, "status": "verified_content", "evidence": "从论文链接的Zenodo v1.0代码包读取Phase_Calculation/Kymograph.tif，395×172 uint16。依作者脚本以0.25h/列标时间；未改值、翻转或平滑。比较图对完整矩阵min–max归一化。具体样本、通道、条件和绝对分化时间未知。", "license": "本地分析记录", "local_path": "data/derived/yaman-2023/provenance.json" } ], "media": [], "missing": [ "Specific sample identity, condition, figure link and channel label not supplied in archive.", "No spatial calibration; TIFF 72 dpi is export metadata, not biological microns.", "No absolute differentiation start time attached to example.", "Some source values are zero; retained unchanged, not imputed or interpreted as missing.", "Matrix is a processed example, not original image stack or biological replicate set.", "Source matrix contains a visible step in intensity near24h; retained unchanged, not cosmetically smoothed." ], "checked": "2026-11-09", "recommendation": "先核实时间、空间与通道，再用于模型定性对照。", "summary": "人轴向类器官中信号梯度与时钟波；作者代码提供示例强度矩阵。", "caveats": [ "Specific sample identity, condition, figure link and channel label not supplied in archive.", "No spatial calibration; TIFF 72 dpi is export metadata, not biological microns.", "No absolute differentiation start time attached to example.", "Some source values are zero; retained unchanged, not imputed or interpreted as missing.", "Matrix is a processed example, not original image stack or biological replicate set.", "Source matrix contains a visible step in intensity near24h; retained unchanged, not cosmetically smoothed." ], "priority": 1, "reporter_short": "HES7–Achilles", "calibration_short": "15 min · 存储行，未标定µm", "availability_status": "verified_content", "availability_summary": "作者示例矩阵已读取并重绘", "availability_filters": [ "数据已读取", "已重绘" ], "verification_scope": "实际数据文件已读取，来源、标定与缺口见处理记录。", "journal": "Cell", "compact_title": "Human clock waves", "kymograph": { "source_url": "https://zenodo.org/records/7458178", "attribution": "数据：Yaman 2023；Clock Explorer 根据实际取得的数据重绘，非原论文面板。", "focus": "同一风格，保留数据边界", "takeaway": "作者示例矩阵已读取并重绘", "reporter": "论文：HES7–Achilles / MESP2–mCherry；此示例通道未标注", "time": "15 min/列；首个存储帧为0，不是分化起点", "space": "存储行0–394；物理标定与方向未注明", "signal": "完整样本独立归一化 · 0–1", "metrics": [ "传播波", "时间尺度" ], "limit": "示例通道与条件未标注；空间是行号，不是µm。", "model_note": "从论文链接的Zenodo v1.0代码包读取Phase_Calculation/Kymograph.tif，395×172 uint16。依作者脚本以0.25h/列标时间；未改值、翻转或平滑。比较图对完整矩阵min–max归一化。具体样本、通道、条件和绝对分化时间未知。", "panel_note": "示例通道与条件未标注；空间是行号，不是µm。", "panel": "Yaman 2023 · Author example", "kind": "experimental", "short": "Kymograph · 数据重绘", "selector": "作者矩阵", "order": 11, "no_original": true, "preview": "figures/comparison/yaman-2023-full.svg", "rendered": { "intensity": { "source_url": "https://zenodo.org/records/7458178", "attribution": "数据：Yaman 2023；Clock Explorer 根据实际取得的数据重绘，非原论文面板。", "focus": "同一风格，保留数据边界", "takeaway": "作者示例矩阵已读取并重绘", "reporter": "论文：HES7–Achilles / MESP2–mCherry；此示例通道未标注", "time": "15 min/列；首个存储帧为0，不是分化起点", "space": "存储行0–394；物理标定与方向未注明", "signal": "完整样本独立归一化 · 0–1", "metrics": [ "传播波", "时间尺度" ], "limit": "示例通道与条件未标注；空间是行号，不是µm。", "model_note": "从论文链接的Zenodo v1.0代码包读取Phase_Calculation/Kymograph.tif，395×172 uint16。依作者脚本以0.25h/列标时间；未改值、翻转或平滑。比较图对完整矩阵min–max归一化。具体样本、通道、条件和绝对分化时间未知。", "panel_note": "示例通道与条件未标注；空间是行号，不是µm。", "panel": "Yaman 2023 · Author example", "preview": "figures/comparison/yaman-2023-full.svg", "downloads": { "svg": "figures/comparison/yaman-2023-full.svg", "pdf": "figures/comparison/yaman-2023-full.pdf", "png": "figures/comparison/yaman-2023-full.png" } } }, "card_context": { "condition": "37°C（方法）", "sample": "示例通道未标注", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10025047/", "evidence": "论文成像方法为37°C；示例未独立标注温度或通道。" }, "comparison": { "short": "Yaman 2023", "reporter": "Author example", "card_title": "作者示例", "reporter_note": "论文 reporter · HES7 / MESP2", "kind": "matrix", "source_label": "作者矩阵", "label": "Author matrix · channel unspecified", "source_url": "https://zenodo.org/records/7458178", "position_unit": "row", "axis_label": "Stored position (row)", "origin": "First stored row; physical scale and direction unspecified", "origin_short": "存储行 · 未标定 µm", "sample": "Unspecified author example", "id": "yaman-2023", "provenance": "data/derived/yaman-2023/provenance.json", "input": "data/derived/yaman-2023/kymograph.npz", "input_sha256": "9e76a9d7f4cd35983373560f44df7d07d8c3ece21bd0d06ccf4ed12c8508b4e6", "shape_space_time": [ 395, 172 ], "time_range_h": [ 0.0, 42.75 ], "spatial_range": [ 0.0, 394.0 ], "missing_values": 0, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 0.0, "max": 4092.0 }, "common_preview": "figures/comparison/yaman-2023-common.svg", "full_preview": "figures/comparison/yaman-2023-full.svg" } } }, { "id": "miao-2023", "short": "Miao 2023", "title": "Reconstruction and deconstruction of human somitogenesis in vitro", "authors": [ "Yuchuan Miao", "Yannis Djeffal", "Alessandro De Simone", "Kongju Zhu", "Jong Gwan Lee", "Ziqi Lu", "Andrew Silberfeld", "Jyoti Rao", "Oscar A. Tarazona", "Alessandro Mongera", "Pietro Rigoni", "Margarete Diaz-Cuadros", "Laura Min Sook Song", "Stefano Di Talia", "Olivier Pourquié" ], "year": 2023, "doi": "10.1038/s41586-022-05655-4", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "species": "Homo sapiens", "species_label": "Human · 人", "systems": [ "in vitro" ], "system_description": "人iPSC来源somitoid / segmentoid", "tissue": "PSM / somitoid", "conditions": "somitoid与segmentoid培养条件不同；具体影片条件见记录", "reporter_construct": "HES7-Achilles、MESP2-mCherry；部分实验同时含UNCX-YFP", "reported_target": "报告基因表达相关信号；不等于绝对分子浓度", "reporter_tags": [ "HES7–Achilles" ], "origin": "live", "origin_label": "真实 time-lapse", "patterns": [ "振荡传播波" ], "time_axis": "h", "space_axis": "按所用样本标定", "time_resolution": "Movie2:15.78 min；Movie8:18 min；Movie10:6 min；不可混用", "space_resolution": "未确认", "replicates": "本轮仅选择一个代表记录，不作为生物学重复统计", "figure_focus": "Fig.1b somitoid；Fig.3l/m segmentoid；Movie2 HES7/MESP2；Movie8 HES7/UNCX/MESP2", "preprocessing": "只取50.500–63.913h的固定40px高条带，将RGB近似映射到ImageJ Green Fire Blue；200µm标尺约115px，空间为图像横坐标。比较横轴显式减50.5h，原始绝对时间保留。 RGB色差>30的像素剔除，空格保留NaN。此阈值是本地分析规则，不是作者数据质量标准。亮部选择性剔除会造成偏差，不用于振幅、细胞或波速定量。", "sources": [ { "id": "S1", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-05655-4/MediaObjects/41586_2022_5655_MOESM7_ESM.mp4", "location": "movie2.mp4", "note": "Downloaded successfully from the public official endpoint; opened locally." }, { "id": "S2", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-05655-4/MediaObjects/41586_2022_5655_MOESM18_ESM.xlsx", "location": "source-fig1.xlsx", "note": "Downloaded successfully from the public official endpoint; opened locally." }, { "id": "S3", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-05655-4/MediaObjects/41586_2022_5655_MOESM20_ESM.xlsx", "location": "source-fig3.xlsx", "note": "Downloaded successfully from the public official endpoint; opened locally." }, { "id": "S4", "url": "https://pmc-oa-opendata.s3.amazonaws.com/PMC10018515.1/PMC10018515.1.xml", "location": "article.xml", "note": "Downloaded and opened; official public endpoint." }, { "id": "S5", "url": "https://raw.githubusercontent.com/imagej/imagej-common/main/src/main/resources/luts/WCIF/Green%20Fire%20Blue.lut", "location": "green-fire-blue.lut", "note": "Downloaded and opened; official public endpoint." }, { "id": "S6", "url": "https://raw.githubusercontent.com/imagej/imagej-common/main/LICENSE.txt", "location": "IMAGEJ-LICENSE.txt", "note": "Downloaded and opened; official public endpoint." }, { "id": "S7", "url": "https://www.nature.com/articles/s41586-022-05655-4#MOESM7", "location": "Methods / figure / video caption", "note": "Video2 is HES7/MESP2 confocal somitoid time-lapse; HES7 Green Fire Blue, MESP2 magenta,15.78min intervals and15fps playback." }, { "id": "S8", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "location": "P8", "note": "HES7 waves propagate from periphery inward with4–5h cycles; reporter ceases around64–72h when MESP2 activates. Motivates early subset." }, { "id": "S9", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "location": "P36", "note": "Laminin-521/polymer substrate,5uM EHT1864, ZeissLSM780 with environment chamber.37C is stated for Segmentoid matrix incubation." }, { "id": "S10", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/#F1", "location": "Methods / figure / video caption", "note": "Fig1b central-line kymograph; source workbook instead contains temporal curves, not that panel's 2D matrix." } ], "field_evidence": { "conditions": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "reporter_construct": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "time_resolution": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "space_axis": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "preprocessing": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ], "figure_focus": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10" ] }, "assets": [ { "level": "matrix", "level_label": "本地重绘矩阵", "label": "视频色阶近似", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "format": "NPZ", "bytes": 154010, "status": "verified_content", "evidence": "视频色阶近似 · 仅定性；早期固定ROI；约25.2%亮部相关像素被排除；不能完全排除混色。", "license": "No open reuse licence identified. PMC author manuscript carries text-mining/fair-use notice; public access is not a CC licence.；ImageJ LUT: BSD 2-Clause", "local_path": "data/derived/miao-2023/kymograph.npz" }, { "level": "document", "level_label": "处理记录", "label": "来源、参数与限制", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "format": "JSON", "bytes": null, "status": "verified_content", "evidence": "只取50.500–63.913h的固定40px高条带，将RGB近似映射到ImageJ Green Fire Blue；200µm标尺约115px，空间为图像横坐标。比较横轴显式减50.5h，原始绝对时间保留。 RGB色差>30的像素剔除，空格保留NaN。此阈值是本地分析规则，不是作者数据质量标准。亮部选择性剔除会造成偏差，不用于振幅、细胞或波速定量。", "license": "本地分析记录", "local_path": "data/derived/miao-2023/provenance.json" }, { "level": "movie", "level_label": "原始附件视频", "label": "Movie 2", "url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-05655-4/MediaObjects/41586_2022_5655_MOESM7_ESM.mp4", "format": "MP4", "bytes": 11351602, "status": "verified_content", "evidence": "已完整解码。对比只采用连续早期窗口；原视频未随交付包分发。", "license": "No open reuse licence identified. PMC author manuscript carries text-mining/fair-use notice; public access is not a CC licence.；ImageJ LUT: BSD 2-Clause" } ], "media": [], "missing": [ "仅50.500–63.913h。正文说明约64–72h MESP2广泛启动，后续帧未纳入。", "早期也不能保证MESP2绝对为零；单LUT残差只能识别明显偏离，不能证明彻底消除混色。", "约25.2%非背景ROI像素被残差阈值排除且集中在亮细胞；约5.2%矩阵格保留NaN。", "固定40px条带未追踪组织或同一细胞，末段偏离几何中心。", "200um标尺换算约1.739um/视频像素，端点有1–2px压缩误差。", "没有将另一Segmentoid成像方法的1.38um采集像素尺度套用至该视频。", "Somitoid实际成像温度未单独注明，不套用基质凝固37C。" ], "checked": "2026-11-09", "recommendation": "先核实时间、空间与通道，再用于模型定性对照。", "summary": "重建人类体节发生，比较时钟波、停止前沿与细胞分选。", "caveats": [ "仅50.500–63.913h。正文说明约64–72h MESP2广泛启动，后续帧未纳入。", "早期也不能保证MESP2绝对为零；单LUT残差只能识别明显偏离，不能证明彻底消除混色。", "约25.2%非背景ROI像素被残差阈值排除且集中在亮细胞；约5.2%矩阵格保留NaN。", "固定40px条带未追踪组织或同一细胞，末段偏离几何中心。", "200um标尺换算约1.739um/视频像素，端点有1–2px压缩误差。", "没有将另一Segmentoid成像方法的1.38um采集像素尺度套用至该视频。", "Somitoid实际成像温度未单独注明，不套用基质凝固37C。" ], "priority": 1, "reporter_short": "HES7–Achilles / MESP2–mCherry", "calibration_short": "15.78 min · 1.74 µm/视频px（约）", "availability_status": "verified_content", "availability_summary": "视频色阶近似 · 仅定性", "availability_filters": [ "数据已读取", "已重绘" ], "verification_scope": "实际数据文件已读取，来源、标定与缺口见处理记录。", "journal": "Nature", "compact_title": "Somitoids and segmentoids", "kymograph": { "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "attribution": "数据：Miao 2023；Clock Explorer 根据实际取得的数据重绘，非原论文面板。", "focus": "同一风格，保留数据边界", "takeaway": "视频色阶近似 · 仅定性", "reporter": "HES7–Achilles为主；MESP2混色不能完全排除", "time": "15.78 min/帧；比较图0对应分化50.5h", "space": "相对视频x=640列的图像横坐标；非A–P轴", "signal": "相对色阶索引 · 非原始荧光强度", "metrics": [ "传播波", "时间尺度" ], "limit": "早期固定ROI；约25.2%亮部相关像素被排除；不能完全排除混色。", "model_note": "只取50.500–63.913h的固定40px高条带，将RGB近似映射到ImageJ Green Fire Blue；200µm标尺约115px，空间为图像横坐标。比较横轴显式减50.5h，原始绝对时间保留。 RGB色差>30的像素剔除，空格保留NaN。此阈值是本地分析规则，不是作者数据质量标准。亮部选择性剔除会造成偏差，不用于振幅、细胞或波速定量。", "panel_note": "早期固定ROI；约25.2%亮部相关像素被排除；不能完全排除混色。", "panel": "Miao 2023 · HES7-dominant signal", "kind": "experimental", "short": "Kymograph · 数据重绘", "selector": "视频色阶近似", "order": 14, "no_original": true, "preview": "figures/comparison/miao-2023-full.svg", "rendered": { "intensity": { "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "attribution": "数据：Miao 2023；Clock Explorer 根据实际取得的数据重绘，非原论文面板。", "focus": "同一风格，保留数据边界", "takeaway": "视频色阶近似 · 仅定性", "reporter": "HES7–Achilles为主；MESP2混色不能完全排除", "time": "15.78 min/帧；比较图0对应分化50.5h", "space": "相对视频x=640列的图像横坐标；非A–P轴", "signal": "相对色阶索引 · 非原始荧光强度", "metrics": [ "传播波", "时间尺度" ], "limit": "早期固定ROI；约25.2%亮部相关像素被排除；不能完全排除混色。", "model_note": "只取50.500–63.913h的固定40px高条带，将RGB近似映射到ImageJ Green Fire Blue；200µm标尺约115px，空间为图像横坐标。比较横轴显式减50.5h，原始绝对时间保留。 RGB色差>30的像素剔除，空格保留NaN。此阈值是本地分析规则，不是作者数据质量标准。亮部选择性剔除会造成偏差，不用于振幅、细胞或波速定量。", "panel_note": "早期固定ROI；约25.2%亮部相关像素被排除；不能完全排除混色。", "panel": "Miao 2023 · HES7-dominant signal", "preview": "figures/comparison/miao-2023-full.svg", "downloads": { "svg": "figures/comparison/miao-2023-full.svg", "pdf": "figures/comparison/miao-2023-full.pdf", "png": "figures/comparison/miao-2023-full.png" } } }, "card_context": { "condition": "温度未注明", "sample": "50.5–63.9 h", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "evidence": "Methods P36 identifies a temperature incubation chamber and CO2 module without an imaging set point. The37 C statement in that paragraph concerns1h Matrigel incubation for Segmentoids, not this Somitoid video." }, "comparison": { "short": "Miao 2023", "reporter": "HES7-dominant signal", "kind": "video_lut", "source_label": "视频色阶近似", "label": "Approx. video color index", "signal_label": "Relative color index", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "roi": "figures/miao-2023/roi-overlay.png", "native_space_only": true, "position_unit": "µm", "origin": "Fixed video column x=640", "origin_short": "固定图像坐标", "axis_label": "Image X (µm)", "sample": "Movie 2 · early subset", "roi_note": "显示实际取样范围及高色差掩膜。仅近似恢复影片色阶；被排除的亮像素会影响强度解释。", "card_title": "HES7 为主", "reporter_note": "仍可能含 MESP2 混色", "time_offset_h": 50.5, "original_time_range_h": [ 50.5, 63.913 ], "coverage_note": "早期 52 帧 · 13.41 h", "id": "miao-2023", "provenance": "data/derived/miao-2023/provenance.json", "input": "data/derived/miao-2023/kymograph.npz", "input_sha256": "7ebdc7256a4b8ed09bfe83d64235789e372da4f431e13a3d170fe9591ec07900", "shape_space_time": [ 520, 52 ], "time_range_h": [ 0.0, 13.412999999999997 ], "spatial_range": [ -452.17391304347825, 450.4347826086956 ], "missing_values": 1398, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 0.7749999761581421, "max": 138.40908813476562 }, "spatial_range_um": [ -452.17391304347825, 450.4347826086956 ], "common_preview": "figures/comparison/miao-2023-common.svg", "full_preview": "figures/comparison/miao-2023-full.svg" } } }, { "id": "shih-2015", "short": "Shih 2015", "title": "Dynamics of the slowing segmentation clock reveal alternating two-segment periodicity", "authors": [ "Nathan P. Shih", "Paul François", "Emilie A. Delaune", "Sharon L. Amacher" ], "year": 2015, "doi": "10.1242/dev.119057", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4440927/", "species": "Danio rerio", "species_label": "Zebrafish · 斑马鱼", "systems": [ "in vivo" ], "system_description": "活体斑马鱼，单细胞Her1-Venus追踪", "tissue": "PSM", "conditions": "23°C；从10–12 somites开始，记录4–6h", "reporter_construct": "Her1–Venus", "reported_target": "报告基因表达相关信号；不等于绝对分子浓度", "reporter_tags": [ "Her1–Venus" ], "origin": "live", "origin_label": "真实 time-lapse", "patterns": [ "振荡传播波" ], "time_axis": "h", "space_axis": "按所用样本标定", "time_resolution": "见所用样本", "space_resolution": "未确认", "replicates": "本轮仅选择一个代表记录，不作为生物学重复统计", "figure_focus": "Figs.1–3：实测单细胞/空间动力学；Fig.4：理想化示意，不能作为实验矩阵", "preprocessing": "本地重绘仅基于实际读取数据；步骤见处理记录。", "sources": [ { "id": "S1", "url": "https://pubmed.ncbi.nlm.nih.gov/25968314/", "location": "Bibliographic record", "note": "Authors,title,Development142(10):1785–1793,2015,DOI." }, { "id": "S2", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4440927/", "location": "Indexed Results and Associated Data (web search readback)", "note": "23°C,4–6h,10–12somites; her1:her1-venus; supplementary HTML657B and PDF6.1MB listed." }, { "id": "S3", "url": "https://pmc-oa-opendata.s3.amazonaws.com/?list-type=2&prefix=PMC4440927", "location": "Official inventory", "note": "HTTP200; KeyCount0, no retrievable public objects." }, { "id": "S4", "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=4440927&retmode=xml", "location": "Front matter/abstract XML", "note": "8976B; no body; PMC open_access=no,manuscript=no." } ], "field_evidence": { "conditions": [ "S1", "S2", "S3", "S4" ], "time_resolution": [ "S1", "S2", "S3", "S4" ], "reporter_construct": [ "S1", "S2", "S3", "S4" ] }, "assets": [ { "level": "raw", "level_label": "原始数据", "label": "连续成像栈 / 细胞强度表", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4440927/", "format": null, "bytes": null, "status": "unknown", "evidence": "未取得原始栈或矩阵，补充PDF/HTML不等同时间序列。", "license": "©2015 The Company of Biologists Ltd; no CC or media-reuse license verified." } ], "media": [], "missing": [ "Original tracked tissue fluorescence matrix or time-lapse image stacks", "Tracking sectors/axis definition and actual time intervals", "Pixel scale applicable to acquired files" ], "checked": "2026-11-09", "recommendation": "先核实时间、空间与通道，再用于模型定性对照。", "summary": "测量前部细胞时钟减慢和时空模式；与Delaune单细胞追踪相衔接。", "caveats": [ "No publicly acquired stack or time-space numeric matrix available for extraction.", "Official eFetch result is front matter and abstract only (no body); not treated as full Methods.", "Indexed supplementary listing shows HTML index and a6.1MB PDF, not a verified movie/matrix. File contents unavailable.", "No matrix was produced from paper images." ], "priority": 3, "reporter_short": "Her1–Venus", "calibration_short": "23°C · 4–6 h", "availability_status": "restricted", "availability_summary": "未取得可重绘时间序列", "availability_filters": [ "正文 / 索引已核", "数值矩阵未取得" ], "verification_scope": "本轮已核公开附件与仓库访问；未取得可解码影片或连续强度矩阵。", "journal": "Development", "compact_title": "Slowing clock dynamics", "kymograph": null } ], "plan": [ { "title": "Rohde 2024 · 连续强度轨迹", "paper": "rohde-2024", "brief": "28.5°C · PSM4队列已按20µm分箱", "paragraphs": [ "可从公开细胞强度和XYZ重新计算，缺失网格保留NaN。", "细胞队列的覆盖边缘不是组织生长前沿；需全组织影像才可扩展至密集时空图。" ], "steps": [ "已完成：连续强度分箱、坐标核对、count与NaN保存。", "已完成：统一绘图和方法/来源卡片。", "若进一步拟合，先区分组织流动、细胞抽样与真实相位传播。" ] }, { "title": "01 · Chhabra 2026：从已有数值kymograph开始", "paper": "chhabra-2026", "brief": "Her7–mVenus · 样本已读取并重绘", "paragraphs": [ "公开仓库提供处理后的强度/phase TIFF。已读取20200815 P1配对：279空间点×119时间点，10min与1.38µm依据Methods及代码参数。原始栈未定位。", "先固定在batch1、27°C、center-of-mass registration；保留处理记录和输入文件hash，不混用不同批次与注册原点。" ], "steps": [ "已完成：从一对处理后TIFF数值重画强度与phase，完整保留279×119数据。未确认此样本为Fig2代表样本。", "下一步：核对有效组织掩码、低信号phase质量与坐标原点，再与模型比较。当前显示相位全矩阵，不把背景相位当作组织波。", "与现有模拟对照周期、空间相位梯度及波向。再决定是否扩展到其他温度与SVD表型；本轮未运行拟合或训练。" ] }, { "title": "01 · Sonnen 2018：先试单通道 ex vivo 波形", "paper": "sonnen-2018", "paragraphs": [ "已完整解码官方MovieS2，保存155帧时间戳并提取平移校正ROI。现可做定性波形比较；原始成像栈仍未定位。", "重绘使用压缩后显示强度。下一步若要估计幅值、速度或参数，需验证有效组织掩码、取线路径及形变配准，优先取得原始数据。" ], "steps": [ "已完成：实际下载、解码、时间/标尺核对、平移校正与ROI矩阵导出。", "核对ROI图与有效组织区；将平移校正扩展到需要的组织坐标，避免把组织运动当作相位传播。", "与一个现有模拟x_i(t,p)并排画；统一轴方向与可比窗口，分别标注实验与模拟。先比较波向、周期和phase gradient，绝不把两图伪彩色当共同浓度尺度。" ], "brief": "Axin2T2A · 已从视频提取并重绘" }, { "title": "02 · Delaune 2012：单细胞轨迹与Notch同步", "paper": "delaune-2012", "paragraphs": [ "次选理由：Her1–Venus、4 min采样与像素标定明确；Paul是共同第一作者，研究问题与细胞同步/分裂密切。原文只明确MATLAB程序可索取，不意味着raw数据已公开或还保存完好。", "前置条件：先核对Movie S1访问与现存荧光/位置矩阵；未来是否向共同作者询问单独讨论。本任务未联系任何人。" ], "steps": [ "若得到细胞强度/坐标表，以time_min、cell_id、position_um、intensity为最小字段；保留谱系和轨迹缺失掩码。", "以组织A–P坐标分箱重画组织kymograph，并同时保留随单细胞轨迹的时间曲线；不要把细胞位移误判为相位传播。", "用同一温度/时标约定与模拟比较单细胞周期、邻居相位差及分裂后恢复；先不进入reward或参数拟合。" ], "brief": "单细胞轨迹 · 需取得数据" }, { "title": "观测模型与停止条件", "paragraphs": [ "建议把实验信号写成I(t,p) = 背景 + 尺度 × reporter响应[x(t,p)] + 噪声。成熟、降解、曝光积分与饱和可改变幅值和相位；一个reporter不能识别整个GRN。此式是本任务的建模建议。", "一旦帧时间、空间尺度或通道身份无法确认，停止定量拟合，只保留定性预览。样本数必须按独立胚胎/培养重复核对；细胞数、frames和pool胚胎数不是可互换的n。", "最小交付应是：原始入口与许可、单样本I(t,p)矩阵、处理脚本与参数、重画实验图、实验/模拟并排图。是否转成GFlowNet reward或拟合目标另行讨论。" ] } ], "pending": [], "background": [ { "title": "François & Mochulska 2024 · Waves, patterns, bifurcations", "url": "https://doi.org/10.1016/j.physrep.2024.05.002", "note": "背景综述，metadata/摘要已核；只用于导航文献，其示意图不计作实验数据。公开preprint：https://arxiv.org/abs/2403.00457" }, { "title": "Qichen Huang · public ISSCR 2026 poster", "url": "https://qichenhuang.com/docs/public-Diverse-Genetic-Circuits-ISSCR2026.pdf", "note": "用户在2026-11-09提供的poster截图（Objectives / Introduction）；完整PDF本次无法由web工具读取。已据截图对照x(p,t)、单细胞轨迹与传播/停止表型。" } ], "poster_reference": { "url": "https://qichenhuang.com/docs/public-Diverse-Genetic-Circuits-ISSCR2026.pdf", "title": "Designing Segmentation Clock Networks with a Generative Model", "basis": "用户在2026-11-09提供的poster截图（Objectives / Introduction）；完整PDF本次无法由web工具读取。", "comparison": [ "传播波", "振荡停止", "相位梯度", "空间条纹" ], "source_citation": "用户poster截图的实验kymograph与Lauschke2013 Fig4a一致（0–40h、0–600µm及波速–投影长度插图），图4c/d为原论文模拟。" }, "screened": [ { "paper": "chhabra-2026", "title": "bioRxiv → PNAS 2026", "note": "已发表；公开数值kymograph，优先候选。" }, { "paper": "ilagan-2011", "title": "Science Signaling 2011", "note": "Notch互补发光方法；无已核体节kymograph。" } ], "comparison": { "checked": "2026-11-09", "color_encoding": { "experimental_intensity": "OrRd", "synthetic_intensity": "Blues", "phase": "twilight_shifted", "intensity_direction": { "experimental": "low values pale cream; high values dark red", "synthetic": "low values light; high values dark blue" }, "no_data_color": "#f1f3f6", "note": "Color distinguishes experimental versus synthetic intensity; retain explicit labels. No synthetic dataset is currently connected.", "colorbar_direction": "low values at bottom; high values at top" }, "datasets": [ { "id": "chhabra-2026", "short": "Chhabra 2026", "reporter": "Her7–mVenus", "kind": "matrix", "label": "Processed matrix", "source_url": "https://github.com/victoria-mochulska/cycles_upon_cycles", "origin": "First stored row", "origin_short": "存储位置", "sample": "27°C · 20200815 P1", "position_unit": "µm", "input": "data/samples/chhabra-2026/Kymo_20200815_P1.tif", "input_sha256": "5d615be397563026e89acf6c030eef61980256ba5686a41a52633bfd4108ea1b", "shape_space_time": [ 279, 119 ], "time_range_h": [ 0.0, 19.666666666666668 ], "spatial_range": [ 0.0, 383.64 ], "missing_values": 0, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 6561.0, "max": 33060.0 }, "spatial_range_um": [ 0.0, 383.64 ], "common_preview": "figures/comparison/chhabra-2026-common.svg", "full_preview": "figures/comparison/chhabra-2026-full.svg" }, { "id": "lauschke-2013", "short": "Lauschke 2013", "reporter": "LuVeLu", "kind": "video", "label": "Video-derived ROI", "source_url": "https://www.nature.com/articles/nature11804", "origin": "ROI start → periphery", "origin_short": "ROI 起点 → 外缘", "sample": "video5", "position_unit": "µm", "roi": "figures/lauschke-2013/video5-roi.jpg", "input": "data/derived/lauschke-2013/video5-kymograph.npz", "input_sha256": "4f391cbfb61f381f7ed132c198682e22acb77e7a92e8cdc1f25ff112b3c16cfd", "shape_space_time": [ 311, 61 ], "time_range_h": [ 0.0, 10.0 ], "spatial_range": [ 0.0, 295.23809523809524 ], "missing_values": 0, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 2.2950307903848715, "max": 223.6760683215834 }, "spatial_range_um": [ 0.0, 295.23809523809524 ], "common_preview": "figures/comparison/lauschke-2013-common.svg", "full_preview": "figures/comparison/lauschke-2013-full.svg" }, { "id": "sonnen-2018", "short": "Sonnen 2018", "reporter": "Axin2T2A", "kind": "video", "label": "Video-derived ROI", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5847172/", "origin": "ROI start → periphery", "origin_short": "ROI 起点 → 外缘", "sample": "movie-s2", "position_unit": "µm", "roi": "figures/sonnen-2018/movie-s2-roi.jpg", "input": "data/derived/sonnen-2018/movie-s2-kymograph.npz", "input_sha256": "d11b72d3b4bfcdb7b89132dcf4c2b72d992399a911d53b6e60f8bc4261234ab2", "shape_space_time": [ 354, 155 ], "time_range_h": [ 0.0, 25.69 ], "spatial_range": [ 0.0, 254.55835989862058 ], "missing_values": 0, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 52.668596285793306, "max": 239.13408927284533 }, "spatial_range_um": [ 0.0, 254.55835989862058 ], "common_preview": "figures/comparison/sonnen-2018-common.svg", "full_preview": "figures/comparison/sonnen-2018-full.svg" }, { "short": "Yaman 2023", "reporter": "Author example", "card_title": "作者示例", "reporter_note": "论文 reporter · HES7 / MESP2", "kind": "matrix", "source_label": "作者矩阵", "label": "Author matrix · channel unspecified", "source_url": "https://zenodo.org/records/7458178", "position_unit": "row", "axis_label": "Stored position (row)", "origin": "First stored row; physical scale and direction unspecified", "origin_short": "存储行 · 未标定 µm", "sample": "Unspecified author example", "id": "yaman-2023", "provenance": "data/derived/yaman-2023/provenance.json", "input": "data/derived/yaman-2023/kymograph.npz", "input_sha256": "9e76a9d7f4cd35983373560f44df7d07d8c3ece21bd0d06ccf4ed12c8508b4e6", "shape_space_time": [ 395, 172 ], "time_range_h": [ 0.0, 42.75 ], "spatial_range": [ 0.0, 394.0 ], "missing_values": 0, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 0.0, "max": 4092.0 }, "common_preview": "figures/comparison/yaman-2023-common.svg", "full_preview": "figures/comparison/yaman-2023-full.svg" }, { "short": "Rohde 2024", "reporter": "Her1–YFP", "kind": "tracks", "source_label": "轨迹分箱", "label": "Tracked cells · 20 µm bins", "source_url": "https://github.com/EPFL-TOP/WSC_NotebooksPaper", "position_unit": "µm", "origin": "each frame's first notochord ROI point, identified as posterior tail-tip reference in author notebook", "origin_short": "细胞队列 · 20 µm", "sample": "PSM4 · Position 2", "roi": "figures/rohde-2024/roi-overlay.png", "coverage_note": "实测 0.25–5.50 h · 211 帧", "roi_note": "150与300min的公开投影图、作者脊索ROI及逆变换后的细胞位置。强度来自CSV；RGB图只用于检查取样几何。", "id": "rohde-2024", "provenance": "data/derived/rohde-2024/provenance.json", "input": "data/derived/rohde-2024/psm4_cohort.npz", "input_sha256": "c91153649cab01f2627235f7d87cafdd960136e5281596ddedefe46f4f5d7617", "shape_space_time": [ 16, 300 ], "time_range_h": [ 0.0, 7.475 ], "spatial_range": [ 10.0, 310.0 ], "missing_values": 3626, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 115.522137771044, "max": 426.423828843253 }, "spatial_range_um": [ 10.0, 310.0 ], "common_preview": "figures/comparison/rohde-2024-common.svg", "full_preview": "figures/comparison/rohde-2024-full.svg" }, { "short": "Sanaki-Matsumiya 2022", "reporter": "HES7–luciferase", "kind": "video_lut", "source_label": "视频色阶近似", "label": "Approx. video color index", "signal_label": "Relative color index", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9050736/", "roi": "figures/sanaki-2022/roi-overlay.png", "native_space_only": true, "position_unit": "video px", "origin": "Per-frame bright-field tissue centroid", "origin_short": "主轴 · 视频像素", "axis_label": "Axial position (video px)", "sample": "Movie 4 · day 4", "roi_note": "显示实际取样范围及高色差掩膜。仅近似恢复影片色阶；被排除的亮像素会影响强度解释。", "coverage_note": "连续段 99 帧 · 16.33 h", "id": "sanaki-2022", "provenance": "data/derived/sanaki-2022/provenance.json", "input": "data/derived/sanaki-2022/kymograph.npz", "input_sha256": "7ddb4dbd492917497bd818920b9461fa4af4194cba7e436cb17835fba361a63e", "shape_space_time": [ 120, 99 ], "time_range_h": [ 0.0, 16.333333333333332 ], "spatial_range": [ -119.0, 119.0 ], "missing_values": 5226, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 2.6666667461395264, "max": 246.19100952148438 }, "common_preview": "figures/comparison/sanaki-2022-common.svg", "full_preview": "figures/comparison/sanaki-2022-full.svg" }, { "short": "Miao 2023", "reporter": "HES7-dominant signal", "kind": "video_lut", "source_label": "视频色阶近似", "label": "Approx. video color index", "signal_label": "Relative color index", "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC10018515/", "roi": "figures/miao-2023/roi-overlay.png", "native_space_only": true, "position_unit": "µm", "origin": "Fixed video column x=640", "origin_short": "固定图像坐标", "axis_label": "Image X (µm)", "sample": "Movie 2 · early subset", "roi_note": "显示实际取样范围及高色差掩膜。仅近似恢复影片色阶；被排除的亮像素会影响强度解释。", "card_title": "HES7 为主", "reporter_note": "仍可能含 MESP2 混色", "time_offset_h": 50.5, "original_time_range_h": [ 50.5, 63.913 ], "coverage_note": "早期 52 帧 · 13.41 h", "id": "miao-2023", "provenance": "data/derived/miao-2023/provenance.json", "input": "data/derived/miao-2023/kymograph.npz", "input_sha256": "7ebdc7256a4b8ed09bfe83d64235789e372da4f431e13a3d170fe9591ec07900", "shape_space_time": [ 520, 52 ], "time_range_h": [ 0.0, 13.412999999999997 ], "spatial_range": [ -452.17391304347825, 450.4347826086956 ], "missing_values": 1398, "normalization": { "method": "linear min-max of finite values in the complete sample", "min": 0.7749999761581421, "max": 138.40908813476562 }, "spatial_range_um": [ -452.17391304347825, 450.4347826086956 ], "common_preview": "figures/comparison/miao-2023-common.svg", "full_preview": "figures/comparison/miao-2023-full.svg" } ], "normalization": "per-sample whole-record finite-value min-max; no percentile clipping", "common_window_h": [ 0, 10 ], "common_space_um": [ 0, 400 ], "full_view": "full native position and time ranges", "source_spatial_origins_are_not_equivalent": true, "script_sha256": "226f3f84eee5585242d9df6fcdfe5f26d0bf132fe7b14149c0993e479f36053f", "exports": { "common": { "pdf": "figures/comparison/all-paper-common.pdf", "svg": "figures/comparison/all-paper-common.svg", "png": "figures/comparison/all-paper-common.png" }, "full": { "pdf": "figures/comparison/all-paper-full.pdf", "svg": "figures/comparison/all-paper-full.svg", "png": "figures/comparison/all-paper-full.png" } }, "figure_table_trace": [ { "artifact_id": "all-paper-common", "source_data": [ { "file": "data/samples/chhabra-2026/Kymo_20200815_P1.tif", "sha256": "5d615be397563026e89acf6c030eef61980256ba5686a41a52633bfd4108ea1b" }, { "file": "data/derived/lauschke-2013/video5-kymograph.npz", "sha256": "4f391cbfb61f381f7ed132c198682e22acb77e7a92e8cdc1f25ff112b3c16cfd" }, { "file": "data/derived/sonnen-2018/movie-s2-kymograph.npz", "sha256": "d11b72d3b4bfcdb7b89132dcf4c2b72d992399a911d53b6e60f8bc4261234ab2" }, { "file": "data/derived/yaman-2023/kymograph.npz", "sha256": "9e76a9d7f4cd35983373560f44df7d07d8c3ece21bd0d06ccf4ed12c8508b4e6" }, { "file": "data/derived/rohde-2024/psm4_cohort.npz", "sha256": "c91153649cab01f2627235f7d87cafdd960136e5281596ddedefe46f4f5d7617" }, { "file": "data/derived/sanaki-2022/kymograph.npz", "sha256": "7ddb4dbd492917497bd818920b9461fa4af4194cba7e436cb17835fba361a63e" }, { "file": "data/derived/miao-2023/kymograph.npz", "sha256": "7ebdc7256a4b8ed09bfe83d64235789e372da4f431e13a3d170fe9591ec07900" } ], "transformation": { "script": "render_comparison.py", "hash": "226f3f84eee5585242d9df6fcdfe5f26d0bf132fe7b14149c0993e479f36053f" }, "caption_claim": "Single-sample experimental records with explicit native calibration and independent display normalization.", "supported_manuscript_claims": [], "limitations": [ "Compressed display values are not raw fluorescence", "Sample registration and local origins differ", "No shared molecular concentration scale", "Single samples do not establish reproducibility" ] }, { "artifact_id": "all-paper-full", "source_data": [ { "file": "data/samples/chhabra-2026/Kymo_20200815_P1.tif", "sha256": "5d615be397563026e89acf6c030eef61980256ba5686a41a52633bfd4108ea1b" }, { "file": "data/derived/lauschke-2013/video5-kymograph.npz", "sha256": "4f391cbfb61f381f7ed132c198682e22acb77e7a92e8cdc1f25ff112b3c16cfd" }, { "file": "data/derived/sonnen-2018/movie-s2-kymograph.npz", "sha256": "d11b72d3b4bfcdb7b89132dcf4c2b72d992399a911d53b6e60f8bc4261234ab2" }, { "file": "data/derived/yaman-2023/kymograph.npz", "sha256": "9e76a9d7f4cd35983373560f44df7d07d8c3ece21bd0d06ccf4ed12c8508b4e6" }, { "file": "data/derived/rohde-2024/psm4_cohort.npz", "sha256": "c91153649cab01f2627235f7d87cafdd960136e5281596ddedefe46f4f5d7617" }, { "file": "data/derived/sanaki-2022/kymograph.npz", "sha256": "7ddb4dbd492917497bd818920b9461fa4af4194cba7e436cb17835fba361a63e" }, { "file": "data/derived/miao-2023/kymograph.npz", "sha256": "7ebdc7256a4b8ed09bfe83d64235789e372da4f431e13a3d170fe9591ec07900" } ], "transformation": { "script": "render_comparison.py", "hash": "226f3f84eee5585242d9df6fcdfe5f26d0bf132fe7b14149c0993e479f36053f" }, "caption_claim": "Single-sample experimental records with explicit native calibration and independent display normalization.", "supported_manuscript_claims": [], "limitations": [ "Compressed display values are not raw fluorescence", "Sample registration and local origins differ", "No shared molecular concentration scale", "Single samples do not establish reproducibility" ] } ] }, "reconstruction_review": [ { "id": "soroldoni-2014", "short": "Soroldoni 2014", "reason": "只有 ROI / LOI 标注，缺少对应像素数据" }, { "id": "tsiairis-2016", "short": "Tsiairis 2016", "reason": "已取附件为单帧 JPG，不能生成时间轴" }, { "id": "shih-2015", "short": "Shih 2015", "reason": "原始栈 / 强度位置表未取得；未用静态图片制造时序。" }, { "id": "delaune-2012", "short": "Delaune 2012", "reason": "原始栈 / 强度位置表未取得；未用静态图片制造时序。" } ], "color_policy": { "experimental_intensity": "OrRd", "synthetic_intensity": "Blues", "phase": "twilight_shifted", "intensity_direction": { "experimental": "low values pale cream; high values dark red", "synthetic": "low values light; high values dark blue" }, "no_data_color": "#f1f3f6", "note": "Color distinguishes experimental versus synthetic intensity; retain explicit labels. No synthetic dataset is currently connected.", "colorbar_direction": "low values at bottom; high values at top" }, "asset_revision": "v7-expanded" }