A plugin for real-time FLIM analysis
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
- OpenScan TCSPC module and all dependencies.
- Verify FLIM electronics are compatible with OpenScan
- Python and the napari package and all dependencies
You can install napari via pip:
pip install napari[all]
You can install napari-live-flim via pip:
pip install napari-live-flim
- In MicroManager, set a port number in the device property setting named
OpenScanFLIM-BH-TCSPC-SendFLIMHistogramsToUDPPort - In Napari, select Plugins > FLIM Viewer (napari-live-flim) to run the plugin. Enter the same port number to connect to OpenScan.
- Begin acquisition within MicroManager.
- Interact with the FLIM data in real-time within napari.
- Modify the FLIM Parameters and Display Filters settings as desired.
- Add selections to the Lifetime Image or Phasor Plot by clicking the relevant New Selection buttons.
- Manipulate the selections with the mouse cursor and modify the selection layer with the layer controls.
- Click the Snapshot button during acquisition to take a snapshot.
- Use the scroll bar under the Lifetime Image to recall a specific snapshot.
- Stop scanning within MicroManager to end acquisition.
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 GNU GPL v3.0 license, "napari-live-flim" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.