Napari Phasors

A comprehensive plugin for phasor analysis in napari. Based on the phasorpy library.

Documentation

Full documentation, including step-by-step guides and the API reference, is available at https://napari-phasors.readthedocs.io.

Features

• Reading a wide range of FLIM and hyperspectral file formats:
  • Raw data formats:
    • .ptu, .fbd, .sdt, .lsm, .tif, .tiff, .czi, .flif, .bh, .b&h, .bhz, .lif, .bin, .json
  • Processed data formats:
    • .ome.tif, .ome.tiff, .r64, .ref, .ifli, .lif, .json
• Phasor analysis on multiple layers simultaneously, including support for stacking multiple raw data files
• Calibration using reference images with known lifetimes
• Filtering with median, wavelet, and automatic thresholding (Otsu, Li, Yen)
• Component analysis for multi-component systems
• Phasor Mapping — colormap apparent/normal lifetime, phasor phase, and phasor modulation per pixel, with interactive 1D histograms, statistics tables, and arc overlay tools
• FRET analysis with donor trajectory visualization and multi-layer donor/background source selection
• Selections via manual drawing, circular/polar/elliptical cursors, and automatic clustering
• Exporting results as OME-TIF or CSV (multiple layers simultaneously)

Installation

You can install napari-phasors via pip. Follow these steps from a terminal.

We recommend using miniforge whenever possible. Click here to choose the right download option for your OS. If you do not use miniforge, but rather Anaconda or Miniconda, replace the mamba term whenever you see it below with conda.

Create a conda environment with napari by typing :

mamba create -y -n napari-phasors-env napari pyqt6 python=3.14 # or 3.12 or 3.13

Activate the environment :

mamba activate napari-phasors-env

Install napari-phasors via pip :

pip install napari-phasors

Alternatively, install latest development version with :

pip install git+https://github.com/napari-phasors/napari-phasors.git

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.

Pre-commit Hooks

This project uses pre-commit to run black, isort, and ruff automatically on every commit. To set it up:

pip install pre-commit
pre-commit install

From now on, every git commit will auto-format and lint your code before the commit goes through. You can also run the hooks manually on all files:

pre-commit run --all-files

License

Distributed under the terms of the BSD-3 license, "napari-phasors" is free and open source software.

Please cite doi: https://doi.org/10.5281/zenodo.14647626 if napari-phasors contributes to a project that leads to a publication.

Issues

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