Size-dependent temporal decoupling of morphogenesis and transcriptional programs in pseudo-embryos

This repository contains data used to generate the results presented in Bennabi et al. 2024. Detailed information about the individual folder content sam_vit\_h\_4b8939.pth file:This file contains the pre-trained weights for the Segment Anything Model (SAM) with a Vision Transformer (ViT) backbone. This can be used to replicate the segmentation of gastruloid in brightfield timelapse movies for the morphological analysis. qPCR_ddct_analysis_actb.csv file: This file contains the RTqPCR data of the biological replicates 1 and 2, including the (Well_Position, Sample_Name, Target_Name, CT, etc.) that were used to generate the graphics in Figure S7 A and B. Figure_1_S1-2:The content in this folder was used to generate the graphs for Figure 1 and the corresponding supplementary Figure S1 and S2. It is split into two main sets of images and data. Included: a Figure_1_movies folder containing brightfield timelapse images of gastruloids for different size conditions in batch 2. a Figure_1_dataframes folder containing the preprocessed dataframes to all analysed movies that can be directly used to recreate all graphs in Figure 1 and S1-2. Not included: live movies of gastruloids for batch 1 and 2 movies and dataframes classified as outlier (excluded from the analysis) Figure_2_S3The here provided data can replicate all all graphs of Figure 2 and the corresponding supplementary Figure S3.It is sorted into two seperate sets of images and data. Included: a Figure_2_movies folder containing 25 live movies of Mesp1/2 gastruloids for different size conditions. per size condition. a Figure_2_dataframes folder containing the preprocessed dataframes to all analysed movies that can be directly used to recreate all graphs in Figure 2 and S2. a configs folder with the configs.yml file specified to facilitate the multipolarity analysis from the dataframes provided in Figure_2_dataframes. Not included: the other half of the live movies of Mesp1/2 gastruloids. movies and dataframes classified as outlier (excluded from the analysis) Note: the provided movies account for about half of the movies per condition that have actually been used for the analysis presented in Figure 2 and S3. The full set of movies would have exceeded the provided storage spece on zenodo. the uploaded movies are not specifically selected, they are the first 25 movies considered for the analysis. the other half of the movies can be made available upon request. Figure_5_S7:The here provided data can replicate all graphs of Figure 5 and the corresponding supplementary Figure S7. Inlcuded: all .tiff (raw) BF images from the two different analysed experiments (zipped file labeled according to the experiment name) used for the analysis from which the raw image analysis is computed. an overviews folder containing figures that provide a visual overview of the imaging data and analysis per experiment and condition. the PH_129_N0_50-1200_exp_combined_shape.json dataframe that contains the preprocessed data from both experiments and can be directly used to recreate all BF based graphs in Figure 5C-F and S7C-G). a configs folder with the configs.yml file specified to facilitate the BF profile analysis from the PH_129_N0_50-1200_exp_combined_shape.json dataframe. the elo_multi_collapse.json dataframe containing the manual annotation of elogation, multipolar, and collapsed gastruloids used in Figure 5E and S7F. Not included: - Figure_6_S8,9:The here provided data can replicate all graphs of Figure 6 and the corresponding supplementary Figure S8 and 9. The data is separated into two parts, one containing immunofluorescent staining for the markers BRA, FOXC1, and SOX2 and one for the markers BRA, FOXC1, MEOX1, and CER1. Both folders contain the following data: Included: the .tiff maximum projections of the individual gastruloid images from the four different analysed experiments (zipped file labeled according to the experiment name) from which the raw image analysis is computed. the df_merged.json dataframe that contains the preprocessed data from all four experiments and can be directly used to recreate all graphs in Figure 6, S8, and S9. a configs folder with the configs.yml file specified to facilitate the IF profile analysis from the df_merged.json dataframe. Not included: the .czi raw image files from which the maximum projections are computed the .tiff maxprojection files that are labeled as „outliers“ (documented in configs/config.yml file) the config files for each individual experiment analysis the .json data frames per condition per experiment the .json data frames per experiment (merged for all conditions) Note: all missing config files and dataframes can be recovered by perfoming the IF_analysis from the start using the github repository linked in the corresponding publication. all .czi raw image files and the .tiff maximum projections of the outliers can be made available upon request.本仓库包含用于复现Bennabi等人2024年发表论文中所得结果的相关数据。 ### 各独立文件夹与文件的详细说明 `sam_vit_h_4b8939.pth`文件：该文件包含搭载视觉Transformer（Vision Transformer, ViT）骨干网络的分割一切模型（Segment Anything Model, SAM）的预训练权重，可用于复现明场延时成像影片中类原肠胚（gastruloid）的分割操作，以支持形态学分析。 `qPCR_ddct_analysis_actb.csv`文件：该文件包含生物学重复1与2的逆转录实时定量PCR（RT-qPCR）数据，包含（孔位、样本名称、靶标名称、CT值等）信息，用于生成补充图S7A与S7B中的可视化图形。 #### Figure_1_S1-2 本文件夹内的内容用于生成图1及其对应的补充图S1、S2的可视化图形，分为图像与数据两大主要模块。 ##### 包含内容： 1. `Figure_1_movies`文件夹：包含批次2中不同尺寸条件下类原肠胚的明场延时成像影片。 2. `Figure_1_dataframes`文件夹：包含所有已分析影片的预处理数据框，可直接用于复现图1与S1-2中的所有可视化图形。 ##### 未包含内容： 批次1与批次2的类原肠胚实时成像影片，以及被归类为异常值（已从分析中排除）的成像影片与数据框。 #### Figure_2_S3 本仓库提供的数据可用于复现图2及其对应补充图S3的所有可视化图形，分为独立的图像与数据两大模块。 ##### 包含内容： 1. `Figure_2_movies`文件夹：包含25个不同尺寸条件下的Mesp1/2类原肠胚实时成像影片，每个尺寸条件对应若干影片。 2. `Figure_2_dataframes`文件夹：包含所有已分析影片的预处理数据框，可直接用于复现图2与S3中的所有可视化图形。 3. `configs`文件夹：内含`configs.yml`配置文件，可辅助基于`Figure_2_dataframes`中提供的数据框进行多极性分析。 ##### 未包含内容： 剩余半数的Mesp1/2类原肠胚实时成像影片，以及被归类为异常值（已从分析中排除）的成像影片与数据框。 --- 注： 1. 本仓库提供的影片仅占图2与S3分析中所用全部影片的一半，完整影片集的容量将超出Zenodo平台的可用存储空间。 2. 上传的影片未经过专门筛选，仅为分析中选取的前25部影片。 3. 剩余半数影片可根据需求另行提供。 #### Figure_5_S7 本仓库提供的数据可用于复现图5及其对应补充图S7的所有可视化图形。 ##### 包含内容： 1. 两个已分析实验的所有明场（Brightfield, BF）原始.tiff图像（以实验名称命名的压缩归档文件），用于从中计算原始图像分析结果。 2. `overviews`文件夹：内含可直观展示各实验与条件下成像数据及分析结果的概览图。 3. `PH_129_N0_50-1200_exp_combined_shape.json`数据框：包含两个实验的预处理数据，可直接用于复现图5C-F与S7C-G中所有基于明场图像的可视化图形。 4. `configs`文件夹：内含`configs.yml`配置文件，可辅助基于`PH_129_N0_50-1200_exp_combined_shape.json`数据框进行明场特征分析。 5. `elo_multi_collapse.json`数据框：包含手动注释的伸长型、多极性及塌陷型类原肠胚数据，用于图5E与S7F的分析。 ##### 未包含内容： 无 #### Figure_6_S8,9 本仓库提供的数据可用于复现图6及其对应补充图S8、S9的所有可视化图形。数据分为两部分：一部分为针对标记物BRA、FOXC1与SOX2的免疫荧光染色数据，另一部分为针对标记物BRA、FOXC1、MEOX1与CER1的免疫荧光染色数据。两个文件夹均包含以下内容： ##### 包含内容： 1. 四个已分析实验的单张类原肠胚图像的最大强度投影.tiff文件（以实验名称命名的压缩归档文件），用于从中计算原始图像分析结果。 2. `df_merged.json`数据框：包含所有四个实验的预处理数据，可直接用于复现图6、S8与S9中的所有可视化图形。 3. `configs`文件夹：内含`configs.yml`配置文件，可辅助基于`df_merged.json`数据框进行免疫荧光特征分析。 ##### 未包含内容： 1. 用于生成最大强度投影的原始.czi图像文件 2. 被标记为“异常值”的.tiff最大强度投影文件（相关信息已在`configs/config.yml`文件中记录） 3. 各单个实验的分析配置文件 4. 各实验按条件划分的.json数据框 5. 各实验（合并所有条件）的.json数据框 --- 注： 1. 所有缺失的配置文件与数据框可通过对应论文中提及的GitHub仓库从头执行免疫荧光分析（IF_analysis）进行恢复。 2. 所有原始.czi图像文件及异常值的.tiff最大强度投影文件可根据需求另行提供。