how do we put fastreseg results back into the pipeline?

Nanostring-Biostats / FastReseg

FastReseg for detection and correction of cell segmentation error based on spatial profile of transcripts.

https://nanostring-biostats.github.io/FastReseg/

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how do we put fastreseg results back into the pipeline? #17

Open patrickjdanaher opened 2 years ago

patrickjdanaher commented 2 years ago

Eventually we'll need to get our results back into the pipeline. What's needed for this?

lidanwu commented 6 months ago

A custom module is added to allow AtoMx pipeline to use FastReseg outputs when only trimming but no merging or new cells allowed. In case of merging or new cells, the cell_id are changed, one would need to create a new study with the post-resegmented data.