README.md

FAIM 3D Organoid Segmentation

This repo contains a collection of scripts which might be useful for 3D organoid segmentation.

infrastructure

In this sub-directory installation instructions/scripts for the different tools are available.

The setup idea is that you would clone this repo and run the the installation scripts in their respective directories. For example for micromamba you would change directory to infrastructure/apps and run the installation script with sh install_micromamba_linux.sh. This will download micromamba and install it into infrastructure/apps/micromamba.

Create environments

After micromamba is installed you must initialize your current command line. Simply copy paste the commands from micromamba initialization.

Once micromamba is initialized you can create the required environment with:

micromamba env create -f infrastructure/environment.yaml

Once the environment is created you can activate it with:

micromamba activate organoid-seg

ipa

Image processing and analysis (ipa) scripts are stored in sub-directories of ipa/

runs

In this directory individual processing run configurations and log-files are stored.

Micromamba initialization

The following commands will initialize the local micromamba (in infrastrucutre/apps) in you current command line. This step must be repeated in every new shell or after every remote login.

export MAMBA_EXE="$(pwd)/infrastructure/apps/micromamba/bin/micromamba"
export MAMBA_ROOT_PREFIX="$(pwd)/infrastructure/apps/micromamba"
export MAMBA_ROOT_ENVIRONMENT="$(pwd)/infrastructure/apps/micromamba"

eval "$($MAMBA_ROOT_ENVIRONMENT/bin/micromamba shell hook -s posix)"

export PIP_CACHE_DIR="$(pwd)/infrastructure/apps/micromamba/PIP_CACHE"

Note: Don't forget to activate the environment with micromamba activate organoid-seg.