DOI: 10.6084/m9.figshare.19729567
title: VistoSeg: processing utilities for high-resolution Visium/Visium-IF images for spatial transcriptomics data (supplementary material)

description: Supplementary material for "<em>VistoSeg</em>: processing utilities for high-resolution Visium/Visium-IF images for spatial transcriptomics data". The bioRxiv pre-print describing VistoSeg is available at https://doi.org/10.1101/2021.08.04.452489. <br> <strong>Supplementary File 1: Human_DLPFC_IF.zip</strong>. This folder contains files to run <em>spotspotcheck </em>on the human DLPFC IF sample. These files are: <strong>scalefactors_json.json.</strong> JSON file from Space Ranger providing the spot diameter estimation in pixels for the high resolution raw histology image. See https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/count for more information about this file. <strong>tissue_positions_list.csv. </strong>CSV file containing spot barcode, if the spot was called under (1) or out (0) of tissue, the array position, image pixel position x, and image pixel position y for the high resolution raw histology image. See https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/count for more information about this file. <strong>tissue_spot_counts.csv. </strong>CSV file containing all the information in tissue_positions_list.csv and also the signal count and percentage area of signal per spot. <strong>V10B01-087_A1_segmentation.mat. </strong>MATLAB mat file consisting segmentations of all channels (AF-Autofluorescence, DAPI, GFAP, NeuN, OLIG2, TMEM119) from the raw TIFF image of human DLPFC stored as V10B01-087_A1.tif <strong>V10B01-087_A1.tif. </strong>Raw multichannel (AF-Autofluorescence, DAPI, GFAP, NeuN, OLIG2, TMEM119) TIFF image of human DLPFC sample used in Figure 4. <strong>Supplementary File 2: Mouse_brain.zip</strong>. This folder contains files to run <em>spotspotcheck </em>on the mouse brain H&E sample. These files are: <strong>scalefactors_json.json.</strong> JSON file from Space Ranger providing the spot diameter estimation in pixels for the high resolution raw histology image. See https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/count for more information about this file. <strong>tissue_positions_list.csv. </strong>CSV file containing spot barcode, if the spot was called under (1) or out (0) of tissue, the array position, image pixel position x, and image pixel position y for the high resolution raw histology image. See https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/count for more information about this file. <strong>V1_Adult_Mouse_Brain_image.tif.</strong> Raw H&E histology image of mouse brain tissue section. <strong>V1_Adult_Mouse_Brain_image_cluster.mat. </strong>MATLAB mat file with different color gradient clusters obtained from V1_Adult_Mouse_Brain_image.tif image. <strong>V1_Adult_Mouse_Brain_image_nuclei.mat. </strong>MATLAB mat file with nuclei segmentation from V1_Adult_Mouse_Brain_image.tif. <strong>Supplementary File 3: Human_heart.zip</strong>. This folder contains files to run <em>spotspotcheck </em>on the human heart H&E sample. These files are: <strong>scalefactors_json.json.</strong> JSON file from Space Ranger providing the spot diameter estimation in pixels for the high resolution raw histology image. See https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/count for more information about this file. <strong>tissue_positions_list.csv. </strong>CSV file containing spot barcode, if the spot was called under (1) or out (0) of tissue, the array position, image pixel position x, and image pixel position y for the high resolution raw histology image. See https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/count for more information about this file. <strong>tissue_spot_counts.csv. </strong>CSV file containing all the information in tissue_positions_list.csv and also the signal count and percentage area of signal per spot. <strong>V1_Human_Heart_image.tif.</strong> Raw H&E histology image of human heart tissue section. <strong>V1_Human_Heart_image_cluster.mat. </strong>MATLAB mat file with different color gradient clusters obtained from V1_Human_Heart_image.tif. <strong>V1_Human_Heart_image_nuclei.mat. </strong>MATLAB mat file with nuclei segmentation from V1_Human_Heart_image.tif