Image Data and Extracted Values for PASTA: Versatile Tyramide-oligonucleotide Amplification for Multi-Modal Spatial Biology

Three .zip archives with image data and processed data from Figs. 1-3, checksums to validate integrity of the folders, and README.txt with instructions.

• Fig1_data:
  • ome.tiff image files for Fig. 1B-D and Fig. S1, S2, S3A
  • MESMER segmentation masks for Fig. 1B-D, Fig. S1, S2
  • Single-cell extracted features based on segmentation masks for Fig. 1B-D, Fig. S1, S2
  • Combined single-cell extracted features each for Fig. 1B-C, 1D, Fig. S1A-B, S1C, S2
  • GEOJSON cropping masks for median pixel calculations, extracted median pixel values, and combined data frame for Fig. S3A
• Fig2_data:
  • ome.tiff/qptiff image files for Fig. 2E and S4D
• Fig3_data:
  • ome.tiff images of all cores for Fig.3 and Fig. S5-8
  • MESMER segmentation masks for all cores for Fig. 3 and Fig. S5-8
  • Single-cell extracted features for all cores for all markers for Fig. 3 and Fig. S5-8
  • GEOJSON files from manual annotation of Hodgkin's tumor cells for Fig. 3 and Fig. S5-8
  • GEOJSON annotation masks for all cores for Fig. 3 and Fig. S5-8
  • Data frames of final annotation, DAPI-normalized combined single-cell features, DAPI-normalized and global percentile scaled combined single-cell features, and fully processed features used for annotation for Fig. 3 and Fig. S5-8
• checksums_Fig1_original.txt
• checksums_Fig2_original.txt
• checksums_Fig3_original.txt
• README.pdf:
  • List of all files
  • Instructions for downloading, unzipping, and checksum validation
  • Instructions for combining with GitHub scripts for figure reproduction

Scripts can be found on https://github.com/SizunJiangLab/PASTA