Deep Learning based image segmentation

Deep Learning based image segmentation#

In this chapter, we will use deep learning based algorithms for image segmentation.

Installation of requirements#

For using cellpose and stardist, these dependencies must be installed:

mamba install cellpose pytorch=1.8.2 cudatoolkit=10.2 -c pytorch-lts
pip install tensorflow
pip install stardist

The notebooks in this folder have been tested using

  • torch==2.0.1

  • stardist==0.8.3

  • tensorflow==2.12.0

  • csbdeep==0.7.3

  • cellpose==2.2.1

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