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Created by Robin Engler@renglerOwner

IMMUCAN output format

Output format specifications for IMMUCAN:

  • sample_name directory: data for each sample is stored in a directory named after the sample. Each directory contains 2 files:

    • sample name + _cell_seg_data.txt: cell segmentation data. REMOVE sample_name col.
    • REMOVE: sample name + _tissue_seg_data_summary.txt: tissue segmentation data.
    • sample name + _summary_statistics.txt: summary table (i.e. content of _summary_table.txt with only the following columns: "tissue_type", "cell_type", "surface_mm2", "cell_density", "cell_count". And only with the rows corresponding to the total sample (i.e. no need for the per-imageID values.

  • parameters.txt: input parameters.

  • log.txt: log of messages/warning generated during the processing.

No .xlsx file.

Edited by Robin Engler