This repository contains the code that accompanies the protocol paper
Müller, Andreas, et al. Organelle-specific segmentation, spatial analysis and visualization of volume electron microscopy datasets
The following subfolders contain code that augment described protocol steps:
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Notebooks relating to the generation of organelle spatial interaction plots
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3D segmentation of golgi apparatus with U-Net
Training and prediction notebooks for a 3D U-Net model for segmentation of golgi aparatus from FIB-SEM volumes
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3D segmentation of secretory granules with
stardist
Training and prediction notebooks for a 3D U-Net stardist model for segmentation of secretory granules from FIB-SEM volumes
Please create a proper conda environment first (see here for a guide).
Then install the following dependencies:
conda install -c conda-forge z5py
pip install -r requirements.txt