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Napari Live Flim

napari-live-flim

A plugin for real-time FLIM analysis

License GNU GPL v3.0 PyPI Python Version tests codecov napari hub

A plugin for real-time FLIM analysis


This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Required dependencies

  • 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]

Installation

You can install napari-live-flim via pip:

pip install napari-live-flim

Usage

  1. In MicroManager, set a port number in the device property setting named OpenScanFLIM-BH-TCSPC-SendFLIMHistogramsToUDPPort
  2. In Napari, select Plugins > FLIM Viewer (napari-live-flim) to run the plugin. Enter the same port number to connect to OpenScan.
  3. Begin acquisition within MicroManager.
  4. 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.
  5. Stop scanning within MicroManager to end acquisition.

Contributing

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.

License

Distributed under the terms of the GNU GPL v3.0 license, "napari-live-flim" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

Version:

  • 0.1.1

Last updated:

  • 14 March 2023

First released:

  • 09 November 2022

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 0
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • dataclasses-json
  • flimlib
  • magicgui
  • matplotlib
  • numpy
  • qtpy
  • scipy
  • superqt
  • vispy

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