Development extended version of the Motile Napari plugin aiming to implement interactive visualization and annotation using a pyqtgraph based lineage tree widget.
Current features include:
- Interactive lineage tree widget connected to a points layer and a tracked labels layer (optional)
- Different display modes to view all nodes or nodes belonging to a lineage
- Option to create or destroy edges that will be included in the next solve.
- Option to change nodes into dividing nodes (Forks, F), endpoints (X), or default nodes (O). Right now this is for visualization only, but will be included in the computation of the next solve in the future.
- Volumetric data can be viewed in two 3D modes: 'volume' and 'plane' (with 1-3 plane sliders)
Browsing data with interactive lineage tree
Viewing planes in 3D
Pinning edges
A plugin for tracking with motile in napari. Motile is a library that makes it easy to solve tracking problems using optimization by framing the task as an Integer Linear Program (ILP). See the motile documentation for more details on the concepts and method.
This plugin depends on motile, which in turn depends on gurobi and ilpy. These dependencies must be installed with conda before installing the plugin with pip.
conda create -n motile-plugin python=3.10
conda activate motile-plugin
conda install -c conda-forge -c funkelab -c gurobi ilpy
Then, to install this development version:
pip install git+https://github.com/AnniekStok/motile_napari_plugin.git
If you encounter any pyqtgraph related problems, please file an issue along with a detailed description.