diff --git a/docs/phasor_approach.rst b/docs/phasor_approach.rst index e6f23600..6104e7b8 100644 --- a/docs/phasor_approach.rst +++ b/docs/phasor_approach.rst @@ -155,7 +155,10 @@ approach to analyze fluorescence time-resolved or spectral images: hyperspectral images. Many `tutorials `_ are available. -- `Spectral Phasor PlugIn `_ +- + .. _phasor_plugins: + + `Spectral Phasor PlugIn `_ and `Time Gated Phasor PlugIn `_ are open-source ImageJ plugins by Farzad Fereidouni, which provide @@ -163,85 +166,144 @@ approach to analyze fluorescence time-resolved or spectral images: images using the phasor approach. The software is distributed under an unknown license and was last updated in 2013. -- `Napari-flim-phasor-plotter `_ +- + .. _napari_flim_phasor_plotter: + + `Napari-flim-phasor-plotter `_ is a napari plugin to interactively load and show raw FLIM single images and series and generate phasor plots. -- `Napari-live-flim `_ +- + .. _napari_live_flim: + + `Napari-live-flim `_ is a napari plugin for real-time TCSPC-FLIM analysis based on FLIMLib. The plugin is distributed under the GPLv3 license. -- `HySP `_ +- + .. _hysp: + + `HySP `_ is a free, closed-source, multi-platform desktop application developed by Francesco Cutrale for the analysis of multi-dimensional, hyper- and multi-spectral data using the phasor approach. -- `FLUTE `_, +- + .. _flute: + + `FLUTE `_, the Fluorescence Lifetime Ultimate Explorer, is an open-source Python GUI for interactive phasor analysis of FLIM data developed by Chiara Stringari and others. The software is distributed under the GPL license. -- `FLIM_tools `_ +- + .. _flim_tools: + + `FLIM_tools `_ is an open-source Python library for linear unmixing and phasor tools for FLIM analysis developed by Jay Unruh. The library is distributed under the GPL2 license. -- `tttrlib `_ +- + .. _tttrlib: + + `tttrlib `_ is an open-source C++ and Python library to read, write, and process time-tagged time-resolved (TTTR) data. It includes functions for computing and correcting phasor coordinates. The library is distributed under the BSD license. -- `PhasorIdentifier `_ +- + .. _phasor_identifier: + + `PhasorIdentifier `_ is a Jupyter notebook to analyze FLIM files, including masking, cell segmentation, pH correlation, nanoscale effects, and precise quantification. The notebook is distributed under CC BY-NC 4.0. -- `FLIMLib `_ is an exponential curve fitting +- + .. _flimlib: + + `FLIMLib `_ is an exponential curve fitting library used for Fluorescent Lifetime Imaging (FLIM). It includes a function to calculate phasor coordinates from time-resolved signals. FLIMLib is licensed under the GPL v3. -- `PAM `_ - is an open-source GUI-based Matlab package for the analysis of fluorescence +- + .. _flimfit: + + `FLIMfit `_ is an open-source, MATLAB-based tool + to analyse and visualize time-resolved data from FLIM measurements + including TCSPC and wide-field time-gated imaging. + It includes a segmentation tool based on the phasor approach. + The affiliated `FlimReader `_ library + provides file readers for FLIM data including TTTR. + FLIMfit is licensed under the GPL v2. + +- + .. _pam: + + `PAM `_ + is an open-source GUI-based MATLAB package for the analysis of fluorescence experiments. The phasor analysis includes region of interests, fractions, triangular mixtures, and FRET estimation. PAM is licensed under the GPL v3. -- `Instant-FLIM-Analysis `_ - is an open-source Matlab program that analyzes data acquired with an +- + .. _instant_flim_analysis: + + `Instant-FLIM-Analysis `_ + is an open-source MATLAB-based program that analyzes data acquired with an "instant FLIM" system. It supports image segmentation based on phasor plot regions of interest and K-means clustering. -- `FLIM Studio `_ +- + .. _flim_studio: + + `FLIM Studio `_ is a commercial software by FLIM LABS, a vendor of portable devices for fluorescence lifetime imaging and spectroscopy. The software provides real-time FLIM phasor-plot analysis, AI-driven phasor-plot analysis techniques, and an application programming interface. Python modules by FLIM LABS are available on `GitHub `_. -- `VistaVision `_ +- + .. _vistavision: + + `VistaVision `_ is a commercial Windows desktop software by ISS, Inc., for confocal microscopy applications, including instrument control, data acquisition, and data processing. It performs image segmentation of FLIM images via the phasor plot. -- `SPCImage `_ +- + .. _spcimage: + + `SPCImage `_ is a commercial Windows desktop software by Becker & Hickl (tm) for TCSPC-FLIM data analysis. It performs image segmentation of time-resolved data via the phasor plot. -- `LAS X `_ +- + .. _lasx: + + `LAS X `_ is a commercial Windows desktop software by Leica Microsystems. The software allows, by using phasors, to follow microenvironmental changes, select components to multiplex signal, and determine FRET efficiency. -- `Luminosa `_ +- + .. _luminosa: + + `Luminosa `_ is a commercial Windows desktop software by PicoQuant GmbH, which includes single molecule detection, FCS, and time-resolved imaging methods. The InstaFLIM module allows simultaneous TCSPC and phasor analysis options for ROI determination. -- `FlimFast `_ +- + .. _flimfast: + + `FlimFast `_ was a research-grade Windows desktop software for frequency-domain, full-field, fluorescence lifetime imaging at video rate, developed by Christoph Gohlke during 2000-2002 at UIUC. It enabled phasor vs intensity