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WayScience / IDR_stream

Software for feature extraction from IDR image data
BSD 3-Clause "New" or "Revised" License
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CP/DP Segmentation Differences #9

Closed roshankern closed 1 year ago

roshankern commented 1 year ago

After comparing the outputs of CP and DP IDR_stream runs, we have discovered that these different IDR_stream packages result in different segmentations. This is likely due to multiple reasons, which will be documented in this issue.

1) CP and DP IDR_stream packages use different versions of CellPose (see env files)

roshankern commented 1 year ago

Through testing we have found a difference in image processing occurs before these images even reach CellPose.

2) Images are being altered in different ways (while consistent in their differences across CP/DP runs) by PyBaSiC illumination correction.

roshankern commented 1 year ago

It appears that PyBaSiC processes the same input slightly differently between idrstream_cp and idrstream_dp environments.

roshankern commented 1 year ago

It is concluded that these differences were caused by using different versions of CellPose and instantiating CellPose with models.Cellpose instead of models.CellposeModel.

roshankern commented 1 year ago

Fixed in https://github.com/WayScience/IDR_stream/pull/12