Gut Analysis Toolbox - automating quantitative analysis of enteric neurons

Luke Sorensen; Adam Humenick; Sabrina SB Poon; Myat Noe Han; Narges S Mahdavian; Matthew C Rowe; Ryan Hamnett; Estibaliz Gomez-de-Mariscal; Peter H Neckel; Ayame Saito; Keith Mutunduwe; Christie Glennan; Robert Haase; Rachel M McQuade; Jaime PP Foong; Simon JH Brookes; Julia A Kaltschmidt; Arrate Mun; Arrate Munoz-Barrutia; Sebastian K King; Nicholas A Veldhuis; Simona E Carbone; Daniel P Poole; Pradeep Rajasekhar

Journal article

Gut Analysis Toolbox - automating quantitative analysis of enteric neurons

Luke Sorensen, Adam Humenick, Sabrina SB Poon, Myat Noe Han, Narges S Mahdavian, Matthew C Rowe, Ryan Hamnett, Estibaliz Gomez-de-Mariscal, Peter H Neckel, Ayame Saito, Keith Mutunduwe, Christie Glennan, Robert Haase, Rachel M McQuade, Jaime PP Foong, Simon JH Brookes, Julia A Kaltschmidt, Arrate Mun, Arrate Munoz-Barrutia, Sebastian K King Show all

Journal of Cell Science | The Company of Biologists | Published : 2024

DOI: 10.1242/jcs.261950

Open access

Abstract

The enteric nervous system (ENS) consists of an extensive network of neurons and glial cells embedded within the wall of the gastrointestinal (GI) tract. Alterations in neuronal distribution and function are strongly associated with GI dysfunction. Current methods for assessing neuronal distribution suffer from undersampling, partly due to challenges associated with imaging and analyzing large tissue areas, and operator bias due to manual analysis. We present the Gut Analysis Toolbox (GAT), an image analysis tool designed for characterization of enteric neurons and their neurochemical coding using two-dimensional images of GI wholemount preparations. GAT is developed in Fiji, has a user-frie..

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University of Melbourne Researchers

DR Myat Noe (Cherish) Han Author

Dr Rachel McQuade Author

Prof Sebastian King Author

DR Pradeep Rajasekhar Author

Related Projects (1)

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Grants

Awarded by European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (EMBO)

Awarded by European Union through the Horizon Europe program

Awarded by National Health and Medical Research Council Australia (NHMRC) Ideas Grant

Awarded by NHMRC Australia Emerging Leader Fellowship

Awarded by National Institutes of Health (NIH) SPARC program

Awarded by NHMRC Australia

Awarded by NHMRC

Awarded by Australian Research Council (ARC) Future Fellowship

Awarded by ARC DECRA Fellow Grant

Funding Acknowledgements

E.G.-d.-M. acknowledges the support of the Gulbenkian Foundation (Fundacao Calouste Gulbenkian) , the European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (EMBO ALTF 174-2022) , and the European Union through the Horizon Europe program (AI4LIFE project with grant agreement 101057970-AI4LIFE) granted to the Optical Cell Biology Group and A.M.-B. M.N.H. acknowledges support from the Melbourne Research Scholarship (The University of Melbourne) and National Health and Medical Research Council Australia (NHMRC) Ideas Grant (GNT1183420) . R.M.M. acknowledges funding by NHMRC Australia Emerging Leader Fellowship (GNT1197245) . A.H. and S.J.H.B. were supported by National Institutes of Health (NIH) SPARC program 1OT2OD24899 to Y. Tache, University of California, Los Angeles. D.P.P. acknowledges support from NHMRC Australia grant 2021675. M.C.R. is supported by Australian Government Research Training Program (RTP) Scholarship. N.S.M. acknowledges funding by FPPS Enhanced Research Experience Scholarship, Monash University, Australia. N.A.V. is supported by NHMRC (APP2021163) and Australian Research Council (ARC) Future Fellowship (FT220100617) . S.E.C. is supported by an ARC DECRA Fellow Grant DE200100825. Open Access funding provided by University of Melbourne. Deposited in PMC for immediate release.