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Automated 3D labelling of fibroblasts and endothelial cells in SEM-imaged placenta using deep learning

Automated 3D labelling of fibroblasts and endothelial cells in SEM-imaged placenta using deep learning
Automated 3D labelling of fibroblasts and endothelial cells in SEM-imaged placenta using deep learning
Analysis of fibroblasts within placenta is necessary for research into placental growth-factors, which are linked to lifelong health and chronic disease risk. 2D analysis of fibroblasts can be challenging due to the variation and complexity of their structure. 3D imaging can provide important visualisation, but the images produced are extremely labour intensive to construct because of the extensive manual processing required. Machine learning can be used to automate the labelling process for faster 3D analysis. Here, a deep neural network is trained to label a fibroblast from serial block face scanning electron microscopy (SBFSEM) placental imaging.
3D image processing, Deep learning, Placenta, SBFSEM images
46-53
SciTePress
MacKay, Benita
318d298f-5b38-43d7-b30d-8cd07f69acd4
Blundell, Sophie
ae6f5834-292d-40fc-8b13-82dc35c66c28
Etter, Olivia
65205ba0-c67e-4125-8455-e325f698d099
Xie, Yunhui
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McDonnell, Michael, David Tom
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Praeger, Matthew
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Grant-Jacob, James
c5d144d8-3c43-4195-8e80-edd96bfda91b
Eason, R.W.
e38684c3-d18c-41b9-a4aa-def67283b020
Lewis, Rohan
caaeb97d-ea69-4f7b-8adb-5fa25e2d3502
Mills, Benjamin
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Soares, Filipe
Fred, Ana
Gamboa, Hugo
MacKay, Benita
318d298f-5b38-43d7-b30d-8cd07f69acd4
Blundell, Sophie
ae6f5834-292d-40fc-8b13-82dc35c66c28
Etter, Olivia
65205ba0-c67e-4125-8455-e325f698d099
Xie, Yunhui
f2c3b0e4-8650-4e04-80e5-04505f45bdd6
McDonnell, Michael, David Tom
bc7b6423-bd77-424d-81e7-4e5448e926cb
Praeger, Matthew
84575f28-4530-4f89-9355-9c5b6acc6cac
Grant-Jacob, James
c5d144d8-3c43-4195-8e80-edd96bfda91b
Eason, R.W.
e38684c3-d18c-41b9-a4aa-def67283b020
Lewis, Rohan
caaeb97d-ea69-4f7b-8adb-5fa25e2d3502
Mills, Benjamin
05f1886e-96ef-420f-b856-4115f4ab36d0
Soares, Filipe
Fred, Ana
Gamboa, Hugo

MacKay, Benita, Blundell, Sophie, Etter, Olivia, Xie, Yunhui, McDonnell, Michael, David Tom, Praeger, Matthew, Grant-Jacob, James, Eason, R.W., Lewis, Rohan and Mills, Benjamin (2020) Automated 3D labelling of fibroblasts and endothelial cells in SEM-imaged placenta using deep learning. Soares, Filipe, Fred, Ana and Gamboa, Hugo (eds.) In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2 BIOIMAGING. SciTePress. pp. 46-53 . (doi:10.5220/0008949700460053).

Record type: Conference or Workshop Item (Paper)

Abstract

Analysis of fibroblasts within placenta is necessary for research into placental growth-factors, which are linked to lifelong health and chronic disease risk. 2D analysis of fibroblasts can be challenging due to the variation and complexity of their structure. 3D imaging can provide important visualisation, but the images produced are extremely labour intensive to construct because of the extensive manual processing required. Machine learning can be used to automate the labelling process for faster 3D analysis. Here, a deep neural network is trained to label a fibroblast from serial block face scanning electron microscopy (SBFSEM) placental imaging.

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Submitted date: 23 October 2019
Accepted/In Press date: 3 December 2019
Published date: 26 February 2020
Additional Information: Publisher Copyright: Copyright © 2020 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserved.
Venue - Dates: BIOSTEC: BIOIMAGING 2020. INSTICC, , Valletta, Malta, 2020-02-24 - 2020-02-26
Keywords: 3D image processing, Deep learning, Placenta, SBFSEM images
Learn more about Zepler Institute for Photonics and Nanoelectronics research Learn more about Zepler Institute for Photonics and Nanoelectronics research Learn more about Institute for Life Sciences research

Identifiers

Local EPrints ID: 436579
URI: http://eprints.soton.ac.uk/id/eprint/436579
DOI: doi:10.5220/0008949700460053
PURE UUID: 350e8346-dae2-4e6f-ba23-e20982dd0f99
ORCID for Benita MacKay: ORCID iD orcid.org/0000-0003-2050-8912
ORCID for Michael, David Tom McDonnell: ORCID iD orcid.org/0000-0003-4308-1165
ORCID for Matthew Praeger: ORCID iD orcid.org/0000-0002-5814-6155
ORCID for James Grant-Jacob: ORCID iD orcid.org/0000-0002-4270-4247
ORCID for R.W. Eason: ORCID iD orcid.org/0000-0001-9704-2204
ORCID for Rohan Lewis: ORCID iD orcid.org/0000-0003-4044-9104
ORCID for Benjamin Mills: ORCID iD orcid.org/0000-0002-1784-1012

Catalogue record

Date deposited: 16 Dec 2019 17:30
Last modified: 17 Mar 2024 03:22

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Contributors

Author: Benita MacKay ORCID iD
Author: Sophie Blundell
Author: Olivia Etter
Author: Yunhui Xie
Author: Michael, David Tom McDonnell ORCID iD
Author: Matthew Praeger ORCID iD
Author: James Grant-Jacob ORCID iD
Author: R.W. Eason ORCID iD
Author: Rohan Lewis ORCID iD
Author: Benjamin Mills ORCID iD
Editor: Filipe Soares
Editor: Ana Fred
Editor: Hugo Gamboa

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