Stardist Conda Environments

This repository hosts .yml files to create conda/mamba environments with stardist, napari and pyclesperanto.

Usage

• Linux
• Windows

Linux

1. Download and install mambaforge for Linux.

   • (optional) In case you have miniforge or miniconda already installed, you can install mamba in the base environment with conda install -c conda-forge mamba.

2. From a terminal, run mamba init once, close that terminal and open a new one (this only has to be done once).

3. Create the new environment with:

   mamba env create -f https://github.com/BiAPoL/stardist-envs/raw/main/stardist-linux.yml

4. Activate the new environment with:

   mamba activate stardist-linux

5. From the activated environment, run the following lines to set the system path (for more information, check here):

   mkdir -p $CONDA_PREFIX/etc/conda/activate.d

   echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/' > $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

   echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/python3.8/site-packages/tensorrt/' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

6. For the above changes to take effect, close the terminal, re-open it and activate the environment again with mamba activate stardist-linux.

7. Clone the Stardist repository to your computer (using GitHub Desktop for example or git commands).

8. Run/modify the example notebooks to your needs through jupyter lab (optionally, open napari and use the stardist-napari plugin).

Windows

1. Download and install mambaforge for Windows.

   • (optional) In case you have miniforge or miniconda already installed, you can install mamba in the base environment with conda install -c conda-forge mamba.

2. Create the new environment with:

   mamba env create -f https://github.com/BiAPoL/stardist-envs/raw/main/stardist-windows.yml

3. Activate the new environment with:

   mamba activate stardist-windows

4. Clone the Stardist repository to your computer (using GitHub Desktop for example or git commands).

5. Run/modify the example notebooks to your needs through jupyter lab (optionally, open napari and use the stardist-napari plugin).

In case you want to remove a conda/mamba environment: mamba env remove -n environment_name