Label-free cell segmentation of diverse lymphoid tissues in 2D and 3D.

Cell reports methods
Authors
Keywords
Abstract

Unlocking and quantifying fundamental biological processes through tissue microscopy requires accurate, segmentation of all cells imaged. Currently, achieving this is complex and requires exogenous fluorescent labels that occupy significant spectral bandwidth, increasing the duration and complexity of imaging experiments while limiting the number of channels remaining to address the study's objectives. We demonstrate that the excitation light reflected during routine confocal microscopy contains sufficient information to achieve accurate, label-free cell segmentation in 2D and 3D. This is achieved using a simple convolutional neural network trained to predict the probability that reflected light pixels belong to either nucleus, cytoskeleton, or background classifications. We demonstrate the approach across diverse lymphoid tissues and provide video tutorials demonstrating deployment in Python and MATLAB or via standalone software for Windows.

Year of Publication
2023
Journal
Cell reports methods
Volume
3
Issue
2
Pages
100398
Date Published
02/2023
ISSN
2667-2375
DOI
10.1016/j.crmeth.2023.100398
PubMed ID
36936072
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