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

Published version
Peer-reviewed

Type

Article

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Authors

Wills, John W 
Robertson, Jack 
Tourlomousis, Pani 
Gillis, Clare MC 
Barnes, Claire M 

Abstract

Unlocking and quantifying fundamental biological processes through tissue microscopy requires accurate, in situ 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.

Description

Keywords

2D, 3D, cell segmentation, confocal microscopy, digital pathology, immunofluorescence, label free, quantitative, single-cell, tissue

Journal Title

Cell Rep Methods

Conference Name

Journal ISSN

2667-2375
2667-2375

Volume Title

3

Publisher

Elsevier BV
Sponsorship
Wellcome Trust (108045/Z/15/Z)
Medical Research Council (MR/R005699/1)