FLIMJ: An open-source ImageJ toolkit for fluorescence lifetime image data analysis
Open Access
- 30 December 2020
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 15 (12), e0238327
- https://doi.org/10.1371/journal.pone.0238327
Abstract
In the field of fluorescence microscopy, there is continued demand for dynamic technologies that can exploit the complete information from every pixel of an image. One imaging technique with proven ability for yielding additional information from fluorescence imaging is Fluorescence Lifetime Imaging Microscopy (FLIM). FLIM allows for the measurement of how long a fluorophore stays in an excited energy state, and this measurement is affected by changes in its chemical microenvironment, such as proximity to other fluorophores, pH, and hydrophobic regions. This ability to provide information about the microenvironment has made FLIM a powerful tool for cellular imaging studies ranging from metabolic measurement to measuring distances between proteins. The increased use of FLIM has necessitated the development of computational tools for integrating FLIM analysis with image and data processing. To address this need, we have created FLIMJ, an ImageJ plugin and toolkit that allows for easy use and development of extensible image analysis workflows with FLIM data. Built on the FLIMLib decay curve fitting library and the ImageJ Ops framework, FLIMJ offers FLIM fitting routines with seamless integration with many other ImageJ components, and the ability to be extended to create complex FLIM analysis workflows. Building on ImageJ Ops also enables FLIMJ’s routines to be used with Jupyter notebooks and integrate naturally with science-friendly programming in, e.g., Python and Groovy. We show the extensibility of FLIMJ in two analysis scenarios: lifetime-based image segmentation and image colocalization. We also validate the fitting routines by comparing them against industry FLIM analysis standards.This publication has 54 references indexed in Scilit:
- Rapid Global Fitting of Large Fluorescence Lifetime Imaging Microscopy DatasetsPLOS ONE, 2013
- Endoscopic Fluorescence Lifetime Imaging for In Vivo Intraoperative Diagnosis of Oral CarcinomaMicroscopy and Microanalysis, 2013
- Fiji: an open-source platform for biological-image analysisNature Methods, 2012
- A Fluorescent Biosensor Reveals Conformational Changes in Human Immunoglobulin E Fc: IMPLICATIONS FOR MECHANISMS OF RECEPTOR BINDING, INHIBITION, AND ALLERGEN RECOGNITIONOnline Journal of Public Health Informatics, 2012
- Metadata matters: access to image data in the real worldThe Journal of cell biology, 2010
- Quantitative analysis of fluorescence lifetime imaging made easyHFSP Journal, 2008
- The Phasor Approach to Fluorescence Lifetime Imaging AnalysisBiophysical Journal, 2008
- Spatially Distinct Binding of Cdc42 to PAK1 and N-WASP in Breast Carcinoma CellsMolecular and Cellular Biology, 2005
- A wide-field time-domain fluorescence lifetime imaging microscope with optical sectioningReview of Scientific Instruments, 2002
- Error Analysis of the Rapid Lifetime Determination Method for Double-Exponential Decays and New Windowing SchemesAnalytical Chemistry, 1999