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 (binlet pawFLIM), 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
• Time-lapse analysis — the phasor plot, histogram and statistics follow napari's own dimension slider (including its play button), with a per-frame statistics table, GIF animation export, and statistics exported pooled or per timepoint
• Exporting results as OME-TIF or CSV (multiple layers simultaneously)
• Batch Analysis — apply the same reading and analysis pipeline (calibration, filtering, masking, component analysis, phasor mapping, FRET, selections) to every file in a folder and export the results headlessly

Installation

There are several ways to install napari-phasors:

Easiest: napari's plugin manager

If you already have napari installed, go to Plugins → Install/Uninstall Plugins..., search for napari-phasors, and click Install.

Standalone installer (no Python required)

Pre-built installers for Windows (.exe), macOS (.dmg), and Linux (.sh) are available on the latest release page. Download and run — no Python installation needed. Installers are ~350–470 MB and bundle everything required.

Using conda (conda-forge)

napari-phasors is available on the conda-forge channel, which installs napari, Qt, and every dependency in one step. We recommend using miniforge. If you use Anaconda or Miniconda, replace mamba with conda.

mamba create -y -n napari-phasors-env -c conda-forge napari-phasors

Activate the environment:

conda activate napari-phasors-env
napari

Using conda + pip

Alternatively, create a plain conda environment and install napari-phasors from PyPI (useful to get a release before it lands on conda-forge):

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

Activate the environment :

conda activate napari-phasors-env
pip install napari-phasors

Development version

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

Contributing

Contributions are very welcome. See the contributing guide for how to set up a development environment, run the tests, and submit a pull request.

This project adheres to a Code of Conduct; by participating, you are expected to uphold it.

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.