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nf-core / molkart

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
https://nf-co.re/molkart
MIT License
10 stars 7 forks source link

Create training subset - uncouple hdf5 / tiff cropping #63

Open kbestak opened 7 months ago

kbestak commented 7 months ago

Description of feature

Currently, cropping the image into tiff files is based on the created crop list created by hdf5 cropping based on the mcmicro-ilastik functionality.

  1. Crops should not be allowed to overlap!
  2. Specifying which file format is wanted should be allowed.
  3. If both formats are provided, the crops should be the same.

Suggestion: new process: find_crops that outputs the coordinates of crops then hdf5 and/or tiff crop creation new process: create crop overview that outputs the crop overview png.