Abstract
flimview is a bio-imaging Python software package to read, explore, manage and visualize Fluorescence-Lifetime Imaging Microscopy (FLIM) images. It can open the standard FLIM data file conventions (e.g., sdt and ptu) and processes them from the raw format to a more readable and manageable binned and fitted format. It allows customized kernels for binning the data as well as user defined masking operations for pre-processing the images. It also allows customized fluorescence decay fitting functions and preserves all of the metadata generated for provenance and reproducibility. Outcomes from the analysis are lossless compressed and stored in an efficient way providing the necessary open-source tools to access and explore the data. flimview is open source and includes example data, example Jupyter notebooks and tutorial documentation. The package, test data and documentation are available on Github.
Highlights
Fluorescence lifetime imaging microscopy (FLIM) is an imaging technique where the image contrast is derived from the differences in the exponential decay rate of the fluorescence from a fluorescent sample (Bower et al, 2018)
In modern two-photon FLIM, the most widely used detection method is known as time-correlated single-photon counting (TCSPC) (Becker et al, 2004)
Fluorescence lifetimes of a fluorophore can be affected by its environment, FLIM have emerged as a valuable tool, providing unique contrast mechanisms for biomedical imaging (Bower et al, 2019; Hirvonen & Suhling, 2016; Ranawat et al, 2019)
Summary
Fluorescence lifetime imaging microscopy (FLIM) is an imaging technique where the image contrast is derived from the differences in the exponential decay rate of the fluorescence from a fluorescent sample (Bower et al, 2018).In modern two-photon FLIM, the most widely used detection method is known as time-correlated single-photon counting (TCSPC) (Becker et al, 2004). Fluorescence lifetime imaging microscopy (FLIM) is an imaging technique where the image contrast is derived from the differences in the exponential decay rate of the fluorescence from a fluorescent sample (Bower et al, 2018). TCPC employs a pulsed excitation source, such as a laser or a light emitting diode and measures the timing of arrival of single photons originating from the fluorescent sample on a detector to reconstruct the fluorescence lifetime decay (McGinty et al, 2016). Fluorescence lifetimes of a fluorophore can be affected by its environment, FLIM have emerged as a valuable tool, providing unique contrast mechanisms for biomedical imaging (Bower et al, 2019; Hirvonen & Suhling, 2016; Ranawat et al, 2019). After compensating for instrument response function, biexponential decay curves are fitted to extract lifetime and amplitude values for two dominant components at each pixel
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