Export ROI Data

1. Navigate to ROI tab

Open the ROI Drawer and choose your export context: - Single ROI: Go to the "ROI" tab to export data for the selected ROI. - Comparsion: Go to the "Compare" tab to export data for a comparison analysis.

2. Export the files

2.1 Export the source data

To export the source data, click the Export button. Then select one or more files from the dropdown to start the download.

Output

Both ROI and Comparsion export options cover the following files:

• GeoJson: a GeoJson file containing the ROI geometry.
• Pixel: a compressed TSV file containing the pixel-level data for this ROI.
• Gene Bulk: A compressed TSV file provides the gene expression data:
  • For single ROI export, it provides the gene expression data for this ROI.

    gene    roi_count   other_count
    Fth1    679 541860
    Mbp 232 378463
    Rplp1   511 265176
    Tmsb4x  629 241168
    

  • For comparison export, it provides the gene expression data for the two ROIs.

    gene    roi1_count  roi2_count  other_count
    Fth1    261 679 541599
    Mbp 240 232 378223
    Rplp1   157 511 265019
    Tmsb4x  99  629 241069
    

2.2 Export the marker genes

To export the marker genes, click the Export button above the marker genes table.

Output

The output tsv file contains 4 columns: Gene, Count, FC (fold change), and Log10P (-log10(p-value)). Genes are ranked by FC in descending order.

Gene    Count   FC  Log10P
Gm15657 1   2,675.049   258,976.435
Gm15351 1   1,337.525   194,086.082
4731419I09Rik   1   668.762 129,195.82
Fbp2    1   445.842 96,750.785