Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order

BMC Bioinformatics
Miles AronEleanor Stride

Abstract

Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually characterized by the generalized polarization (GP) parameter. With the development of commercial microscopes equipped with spectral detectors, spectral imaging has become a convenient and powerful technique for measuring GP and other membrane properties. The existing tools for spectral image processing, however, are insufficient for processing the large data sets afforded by this technological advancement, and are unsuitable for processing images acquired with rapidly internalized fluorescent probes. Here we present a MATLAB spectral imaging toolbox with the aim of overcoming these limitations. In addition to common operations, such as the calculation of distributions of GP values, generation of pseudo-colored GP maps, and spectral analysis, a key highlight of this tool is reliable membrane segmentation for probes that are rapidly internalized. Furthermore, handling for hyperstacks, 3D reconstruction and batch processing facilitates analysis of data sets generated by time series, z-stack, and area scan microscope operations....Continue Reading

References

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Citations

Sep 8, 2019·Scientific Reports·Manjari MishraShobhna Kapoor
Apr 27, 2018·Chemical Communications : Chem Comm·Eli SlendersMarcel Ameloot
Apr 16, 2020·International Journal of Molecular Sciences·Bingen G MonasterioAlicia Alonso
Nov 30, 2019·Nature Communications·Jesse A Rudd-SchmidtIlia Voskoboinik
Dec 11, 2020·Journal of Cell Science·Indranil GhoshSiddhartha S Jana
Sep 14, 2019·Langmuir : the ACS Journal of Surfaces and Colloids·Miles AronEleanor Stride
Nov 30, 2018·Langmuir : the ACS Journal of Surfaces and Colloids·Joshua OwenEleanor Stride

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Software Mentioned

ImageJ
SimFCS
Windows
Formats Library
OME
Spectral Imaging Toolbox
Bio
MATLAB
Globals
TIFF

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