This template repository contains the first two processing steps for any Single Worm Imaging project. In the first step, the raw data is converted to ome-zarr and in the second step the worm segmentation is performed. Further processing steps can be added to the workflow.
HELP: Please reach out to FAIM if you have any questions or need help with setting up the project.
This repository is a template repository. To create a copy of this repository, click on the green "Use this template" button on the top right of the repository page.
After creating a copy of the repository, clone the repository to your local machine and to the fileserver. The copy on the fileserver is used for the processing of the data, whereas the local copy is used to visualize and annotate the data.
Once the repository is cloned, the documentation can be rendered with the following command:
pixi run build_docs
Running this command for the first time can take a while. After the command has finished, the documentation can be viewed by opening the sites/index.html file in a web browser. To run the processing follow the How-to Guide section in the documentation.
This project was generated with the faim-ipa-project copier template.