Set of napari widgets to interactively proofread, edit, and annotate, cell tracking data tracked with Ultrack.
TrackEdit napari UI:
- Clone repo in $MYDATA and install pixi environment
git clone https://github.com/royerlab/trackedit.git --recurse-submodules
cd trackedit
module load pixi
pixi install
pixi shellAlternatively, you can activate the environment using conda conda activate .pixi/envs/default (after pixi install)
cdto relevant data folder (that containsdata.dbandmetadata.toml), copyscripts/demo.pyscript, change relevant input parameters, and run inTRACKtive:
python demo_neuromast.py #_after changing relevant parameters
Note: make sure to first pixi shell in the $MYDATA directory, before running the python script. This is the equivalent of conda activate ...
| Mouse / Key binding | Action |
|---|---|
| Click on point/label | Select node (centers view if needed) |
| SHIFT + click | Add node to selection |
| Q | Toggle between all nodes view and selected lineages only |
| V | Toggle visibility of all tracking layers (points, labels, tracks) |
| Mouse / Key binding | Action |
|---|---|
| Click on node | Select node (centers view if needed) |
| SHIFT + click | Add node to selection |
| Scroll | Zoom in/out |
| Scroll + X / Right click + drag horizontally | Zoom x-axis only |
| Scroll + Y / Right click + drag vertically | Zoom y-axis only |
| Mouse drag | Pan |
| SHIFT + Mouse drag | Rectangular node selection |
| Right click | Reset view |
| Q | Toggle between all lineages (vertical) and selected lineages (horizontal) |
| T | Select all nodes of the tracks to which to currently selected node belongs too |
| ← | Select node to the left |
| → | Select node to the right |
| ↑ | Select parent node (vertical) or next lineage (horizontal) |
| ↓ | Select child node (vertical) or previous lineage (horizontal) |
| Mouse / Key binding | Action |
|---|---|
| D | Delete selected nodes |
| B | Break edge between selected nodes |
| A | Create edge between selected nodes (if valid) |
| Z | Undo last edit |
| R | Redo last edit |
To run the TrackEdit tests (ignore the motile_tracker tests) as individual napari instances to prevent the widgest from interfering with each other:
pytest _tests/ --forked
The TrackEdit widget structure is inspired by, and built upon, Motile_tracker (Funke lab, HHMI Janelia Research Campus)
trackedit is distributed under the terms of the MIT license.