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This repository has been archived by the owner on Aug 13, 2024. It is now read-only.

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This repo has been superseeded by ConfluentFUCCI and is now archived

Please check out the now peer-reviewed ConfluentFUCCI or the accomnying paper

MicroscopyPipeline

Left empty on purpose

Pipeline

  1. Split channels (phase, C1, C2)
  2. Normalize histogram (CLAHE) individually per channel
  3. Feed C1, C2 into ilastik using pretrained pipline to create probability maps
  4. Feed probability maps CellProfiler using predefined pipeline