Tools

export_tiff.py

  • Converts CosMx spatial transcriptomics image data from Zarr format to multiscale OME-TIFF

  • Supports selecting specific imaging channels, optionally includes segmentation label edge maps, and embeds spatial metadata such as pixel size and contrast limits

  • Channels are grouped into batches, processed with Dask for scalability, and written to OME-TIFF using tifffile, producing a tiled, compressed, pyramid image stack

make_composite_revised_image.py

  • Processes layered 2D morphology TIFF images by extracting individual channels, converting them to 8-bit grayscale, applying optional autocontrast, and generating colorized composite images

  • Validates user input for clipping percentage and output format, ensures required folders exist, and handles exceptions for folder conflicts or invalid input

  • Supports JPG, PNG, and TIFF formats, and creates both raw and enhanced composite outputs using predefined color mappings.

remove_slice_tiff.py

  • Removes a specific slice (index 4) from multi-layer .TIF files in a folder and saves the modified files to an output directory.

CellLabels.sh

  • Copies all CellLabels *.tif files from subdirectories into a single destination folder, extracts compressed .csv.gz files, and renames any *-polygons.csv files by replacing hyphens with underscores for consistency.

renaming_composite.sh

  • Renames files in a specified directory by removing _composite or _composite_autocontrast from filenames and replacing the first occurrence of F with CellComposite_F, then outputs the changes made.

Xenium_data.xlsx

  • XLSX table explaining each Xenium data output and which files are important for visualization, analysis, and re-preprocessing.