steinbock results of IMC example data

This repository hosts the results of processing example imaging mass cytometry (IMC) data hosted at zenodo.org/record/5949116 using the steinbock framework available at github.com/BodenmillerGroup/steinbock. Please refer to steinbock.sh for how these data were generated from the raw data. The following files are part of this repository: panel.csv: contains channel information regarding the used antibodies in steinbock format img.zip: contains hot pixel filtered multi-channel images derived from the IMC raw data. One file per acquisition is generated images.csv: contains metadata per acquisition pixel_classifier.ilp: ilastik pixel classifier (same as the one in zenodo.org/record/6043544) ilastik_crops.zip: image crops on which the ilastik classifier was trained (same as the ones in zenodo.org/record/6043544) ilastik_img.zip: contains multi-channel images (one per acquisition) in .h5 format for ilastik pixel classification ilastik_probabilities.zip: 3 channel images containing the pixel probabilities after pixel classification masks_ilastik.zip: segmentation masks derived from the ilastik pixel probabilities using the cell_segmentation.cppipe pipeline masks_deepcell.zip: segmentation masks derived by deepcell segmentation intensities.zip: Contains one .csv file per acquisition. Each file contains single-cell measures of the mean pixel intensity per cell and channel based on the files in img.zip and masks_deepcell.zip. regionprops.zip: Contains one .csv file per acquisition. Each file contains single-cell measures of the morphological features and location of cells based on masks_deepcell.zip. neighbors.zip: Contains one .csv file per acquisition. Each file contains an edge list of cell IDs indicating cells in close proximity based on masks_deepcell.zip. ome.zip: contains .ome.tiff files derived from img.zip; one file per acquisition histocat.zip: contains single-channel .tiff files with segmentation masks derived from masks_deepcell.zip for upload to histoCAT (bodenmillergroup.github.io/histoCAT) cells.csv: contains intensity and regionprop measurements of all cells cells_csv.zip: contains intensity and regionprop measurements of all cells per acquisition cells.fcs: contains intensity and regionprop measurements of all cells in fcs format cells_fcs.zip: contains intensity and regionprop measurements of all cells per acquisition in fcs format cells.h5ad: contains intensity, regionprop and neighbor measurements of all cells in anndata format cells_h5ad: contains intensity regionprop and neighbor measurements of all cells per acquisition in anndata format graphs.zip: contains spatial object graphs in .graphml format; one file per acquisition本仓库存储了对zenodo.org/record/5949116平台上的成像质谱流式细胞术（imaging mass cytometry, IMC）示例数据，使用github.com/BodenmillerGroup/steinbock提供的steinbock框架处理后得到的结果。有关如何从原始数据生成此类结果，请参考steinbock.sh脚本。本仓库包含以下文件： panel.csv：包含采用steinbock格式的抗体通道相关信息 img.zip：包含从IMC原始数据经热像素滤波得到的多通道图像，每个采集任务对应一个文件 images.csv：包含每个采集任务的元数据 pixel_classifier.ilp：ilastik像素分类器（与zenodo.org/record/6043544中的分类器一致） ilastik_crops.zip：包含训练该ilastik分类器所用的图像裁剪块（与zenodo.org/record/6043544中的裁剪块一致） ilastik_img.zip：包含用于ilastik像素分类的多通道图像（每个采集任务一个文件），格式为.h5 ilastik_probabilities.zip：包含像素分类完成后得到的3通道像素概率图像 masks_ilastik.zip：包含通过cell_segmentation.cppipe管线，从ilastik像素概率结果导出的细胞分割掩码 masks_deepcell.zip：包含通过DeepCell分割得到的细胞分割掩码 intensities.zip：包含每个采集任务对应的一个.csv文件，每个文件基于img.zip与masks_deepcell.zip中的文件，统计了每个细胞各通道的平均像素强度的单细胞测量数据 regionprops.zip：包含每个采集任务对应的一个.csv文件，每个文件基于masks_deepcell.zip中的文件，统计了细胞的形态特征与空间位置的单细胞测量数据 neighbors.zip：包含每个采集任务对应的一个.csv文件，每个文件基于masks_deepcell.zip中的文件，提供了指示邻近细胞关系的细胞ID边列表 ome.zip：包含从img.zip导出的.ome.tiff格式文件，每个采集任务对应一个文件 histocat.zip：包含从masks_deepcell.zip导出的单通道.tiff格式分割掩码文件，用于上传至histoCAT平台（bodenmillergroup.github.io/histoCAT） cells.csv：包含所有细胞的强度与区域属性测量数据 cells_csv.zip：包含每个采集任务对应的所有细胞的强度与区域属性测量数据 cells.fcs：包含所有细胞的强度与区域属性测量数据，格式为FCS cells_fcs.zip：包含每个采集任务对应的所有细胞的强度与区域属性测量数据，格式为FCS cells.h5ad：包含所有细胞的强度、区域属性与邻域关系测量数据，格式为AnnData cells_h5ad：包含每个采集任务对应的所有细胞的强度、区域属性与邻域关系测量数据，格式为AnnData graphs.zip：包含每个采集任务对应的一个.graphml格式的空间对象图文件