Image registration pipeline for large volume EM and LM datasets, built on multiview-stitcher, with a napari plugin, a command-line pipeline and Jupyter notebooks.
Main documentation: ccp-volume-em.github.io/muvis-align
Generated documentation: deepwiki.com/ccp-volume-em/muvis-align
The napari plugin can run in a container on a Slurm cluster (HPC), shown in your browser through Xpra, without
installing Python or muvis-align yourself. This needs Apptainer on the cluster, ssh access to its login node
(preferably with an ssh key), and the xpra-*.sh scripts together in one folder on your own machine: download this
repository as a ZIP and unzip it, or
clone it.
From your own machine, one command builds the container on the cluster if needed, starts the job, and opens napari
in your browser (on Windows in Git Bash, or as .\xpra-connect.sh ... from PowerShell):
bash xpra-connect.sh <user>@<login node> [folder on the cluster, default: muvis-align] [--pull]
Or step by step, on the cluster's login node in a folder with xpra-pull.sh and xpra-run.sh:
bash xpra-pull.sh # once, and to update the container
bash xpra-run.sh # starts the job and prints how to connect from your own machine
See the documentation for details.
The simplest way: in napari, open Plugins > Install/Uninstall Plugins..., search for muvis-align and
install it. It is listed on the napari hub.
muvis-align needs Python 3.12 or later. Install it via pip:
pip install muvis-align
To install muvis-align with napari and Qt, and the optional registration methods (Elastix, ANTs
and CPD), use:
pip install "muvis-align[all]"
The command-line script, example parameter files and notebooks are in this repository, not the pip package: see the documentation.
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
Distributed under the terms of the MIT license, "muvis-align" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
This napari plugin was generated with copier using the napari-plugin-template.