napari-flim-phasor-plotter

Here you find documentation for the napari-flim-phasor-plotter plugin, a napari plugin to interactively load and show raw fluorescence lifetime imaging microscopy (FLIM) single images and series and generate phasor plots. These are Fourier transforms of the decay data being visualized using the napari-clusters-plotter plotter, adapted to suit the FLIM context. This allows qualitative and quantitative downstream analysis of FLIM images.

Quick demo

Installation

We recommend installing napari-flim-phasor-plotter with mamba after having Miniforge installed in your computer. Follow these steps from a terminal.

Click here to choose the right download option for your OS after clicking on the latest release.

Create a conda environment:

mamba create -n napari-flim-phasor-env python=3.10 napari pyqt git

Activate the environment:

mamba activate napari-flim-phasor-env

Install napari-flim-phasor-plotter plugin with:

pip install napari-flim-phasor-plotter

Alternatively, clone this repository and install the latest plugin development version with:

pip install git+https://github.com/zoccoler/napari-flim-phasor-plotter.git

Table of Contents

Here is an automatically generated Table of Contents:

Usage

• Opening Raw FLIM Data
• Data Conversion
• Phasor Analysis
• Integrating Phasor Analysis into a Workflow
• Saving Results

Examples

• FLIM Workflow Example

API Reference

• Sample Data API
• Widgets API
• Phasors API
• Filters API
• Convert Module API

Limitations / Future Work

The plugin does not yet support:

• Round cluster selection or cursor selection (only free-hand selection is available)

• Pseudo-channel generation from selected clusters in the phasor plot

• FRET analysis

• Tile processing

• Fitting of decay curves