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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
83 stars 35 forks source link

ilastik project #36

Closed SchulzDan closed 4 years ago

SchulzDan commented 4 years ago

hi, because I have now had the issue myself, that if the data used for ilastik training changed directory, or the training itself moved to another directory, the project is not usable any more if it was setup with absolute paths. Since it appears to me that absolute paths are the default input for ilastik I recommend that we add a section to the desription and recommend storing "relative paths". then one can simply always copy data and ilastik project to other locations and they will still work.

votti commented 4 years ago

Hey @SchulzDan,

This is an important point and I think the Relative paths are also the default in newer Ilastik versions. However, note that relative paths are not possible in Windows if the data and the project arent in the same drive.

In case you are stuck with an ilastik project with broken paths, it is also always possible to change the Ilastik project file, as this is a standard .hdf5 format. (Maybe here some pointers how to open it in python: https://github.com/BodenmillerGroup/bbsnippets/blob/fix-ilastikexample/snippets/image_analysis/ilastik_projects/ilastik_projects.ipynb)