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dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics
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Errors related to rust sorting #41

Closed RitaRuoxinLi closed 3 weeks ago

RitaRuoxinLi commented 4 weeks ago

Hi, I am trying proseg on our newly generated tissue samples, so far it works great and I am very appreciative of the effort. However, for only one of the samples generated, the xenium ranger seems running fine, but when applying proseg on the transcript.parquet, I got the following errors:

Screenshot 2024-10-29 at 1 00 12 PM

Proseg has being running fine on other samples, but only failed for this one, and the Xenium ranger's output looks normal(median # transcripts per cell is 273) could you please provide some hints on how to resolve the issue?

I will be very appreciative!

dcjones commented 4 weeks ago

I believe this issue was fixed in version 1.1.7. Please check that you're using the latest version of proseg (proseg --version should tell you).

RitaRuoxinLi commented 4 weeks ago

Thank you for your reply! I went back to check proseg --version, it is already proseg 1.1.8

dcjones commented 4 weeks ago

Oh, I see! It is the same error, but in a different place. I've just published version 1.1.9 which I believe should fix this.

RitaRuoxinLi commented 3 weeks ago

I tested version 1.1.9 and the error is already resolved, thank you very much for your assistance!