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BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
50 stars 15 forks source link

Reproducibility across releases #130

Closed nilseling closed 2 years ago

nilseling commented 2 years ago

Hi @jwindhager

again, this is more to track this issue rather than a real "issue". I have now run steinbock twice each using v0.13.5 and v0.14.1. Using the same version I can recover exactly the same cells (at least the number of cells match) but I do get different numbers of cells when comparing between the different release. Do you know why this is and if that can be fixed somehow? I'm using deepcell segmentation.

jwindhager commented 2 years ago

Hi @nilseling! Indeed, with steinbock v0.14.0, deepcell was upgraded from version 0.11.0 to 0.12.0 (see here), which included an update of the trained models (see here). I'm afraid there is no way to recover the same number of cells across versions, but you can always use multiple versions for the individual steps.