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High fraction of cells empty - alert from xeniumranger after import

Open imran-aifi opened this issue 7 months ago • 2 comments

When running proseg on Xenium data and following the Xenium Explorer tutorial, I get a high fraction of cells empty as reported by the xeniumranger QC report:

High fraction of cells empty | 18.2% | This alert is triggered when the value is >= 10.0%. An unusually high fraction of segmented cells were found to contain no transcripts. Check the cell segmentation. Total number of cells (153000) and median transcripts per cell (23) are comparable to the original xeniumranger results using Xenium's older nuclear expansion segmentation.

I am running proseg with proseg --xenium --ncomponents 10 as the only parameters used. I'm wondering if you had recommended parameters, or guidance on whether to use --voxel-layers 1 to simplify the segmentation as we do not have serial sections for 3D spatial transcriptomics.

imran-aifi avatar Jul 10 '24 00:07 imran-aifi