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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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Error in loading ISS data in quick start tutorial #2013

Open rocketeer1998 opened 3 months ago

rocketeer1998 commented 3 months ago

Because of the updating version of scikit-image, from starfish import data throws an ImportError. We need to fix three files:

  1. In site-packages\starfish\core\image\_registration\LearnTransform\translation.py, change from skimage.feature.registration_translation into skimage.registration.phase_cross_correlation
  2. In site-packages\starfish\core\morphology\Filter\min_distance_label.py, change from skimage.morphology.watershed into skimage.segmentation.watershed
  3. In site-packages\starfish\core\morphology\Segment\watershed.py, change from skimage.morphology.watershed into skimage.segmentation.watershed
rocketeer1998 commented 3 months ago

And why not update the corresponding arguments in the most recent release?

shachafl commented 1 week ago

@rocketeer1998 there is an open PR #2009 that addresses this and needs to be reviewed and merged into the master branch. For now you can either: 1) For scikit-image 0.21, fork my branch: git clone -b python3.8 https://github.com/shachafl/starfish.git 2) For scikit-image 0.18.3, use the master branch in a clean virtual environment and execute make install-dev