Protocol Notebooks

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:

1. Organelle Interaction Plots

   

   Notebooks relating to the generation of organelle spatial interaction plots

2. 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

3. 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

Installation

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