Daniel C. Jones
Daniel C. Jones
Strange, I'm not sure what would explain that regression. I can try running it and see how it works for me. Is this the dataset? https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/cosmx-smi-human-pancreas-ffpe-dataset/
That's peculiar. There may be a very small number of cells dropped in the conversion. I would check that the analysis_summary.html matches what's in baysor-cell-polygons.geojson. You can count polygons in...
This conversion will drop any cells that have no assigned transcripts, since that causes issues with xenium ranger. That's likely what you are seeing here. It's typically a very small...
This should be fixed with proseg 3.0.5, which I published just now.
That's odd, could you post the exact error message you get?
This looks like a different error, and judging from the line numbers an older version of proseg (you can check with `proseg --version`). That probably doesn't matter though because the...
Could you post the version you're using (run `proseg --version`)?
Hi Jaspreet, Thanks for trying out proseg! 1. Proseg optimizes boundaries of a fixed number of cells that are provided in prior segmentation. Usually this is from prior segmentation done...
Thanks for tying proseg. It's not obvious to me what's going wrong with your data, I'm afraid. Proseg will by default filter out transcripts that have a qv score lower...
Hi Raphael, I'll try to clarify things if I can: > So is this a third matrix, under bad segmentation, how does one obtain such a segmentation? And how is...