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For the complete documentation index, see llms.txt. This page is also available as Markdown.

Data for ICM

This page describes the files located in {SampleID}_ICM.tar.gz.

Each set of binned data (cell, grid, and optionally nuclei) for each sample has the following files for import into ICM. Each sample has a Manifest file that contains all the file information for loading into ICM.

  • .h5ad (main output file; see format below)

  • clustered.row.annotation *

  • pca.col.matrix *

  • pca.h5ad * (see format below)

  • pca.row.annotation *

  • filtered.effective_lib_sizes.txt

  • filtered.row.index

  • raw.row.annotation

  • raw.col.matrix

  • raw.col.annotation

  • raw_stats.txt

  • raw.effective_lib_sizes.txt

  • normalized.h5ad (see format below)

  • umap.col.matrix

  • umap.h5ad (see format below)

* These are not produced when running on the local DAM App or when the "Skip Tertiary" option is selected when running on the cloud.

H5AD format

H5AD is an HDF5 file storing AnnData objects. The detailed format definition can be found at https://github.com/scverse/anndata/blob/main/docs/fileformat-prose.md.

H5AD has specific requirements for file, group, and dataset attributes so that third-party tools can recognize it. Here is the current implementation.

Normalized H5AD

PCA H5AD

UMAP H5AD

PreviousCell and Nuclei Contours CSVs
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