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A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations

Cell culture is undeniably important for multiple scientific applications, including pharmaceuticals, transplants, and cosmetics. However, cell culture involves multiple manual steps, such as regularly analyzing cell images for their health and morphology. Computer scientists have developed algorith...

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Main Authors: Malik, Hafizi, Idris, Ahmad Syahrin, Toha @ Tohara, Siti Fauziah, Mohd Idris, Izyan, Daud, Muhammad Fauzi, Azmi, Nur Liyana
Format: Article
Language:English
English
Published: PeerJ, Inc. 2023
Subjects:
T Technology (General)
TA168 Systems engineering
Online Access:http://irep.iium.edu.my/104688/3/104688_A%20review%20of%20open-source.pdf
http://irep.iium.edu.my/104688/9/104688_A%20review%20of%20open-source_Scopus.pdf
http://irep.iium.edu.my/104688/
https://peerj.com/articles/cs-1364/
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spelling my.iium.irep.1046882023-06-21T07:17:48Z http://irep.iium.edu.my/104688/ A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations Malik, Hafizi Idris, Ahmad Syahrin Toha @ Tohara, Siti Fauziah Mohd Idris, Izyan Daud, Muhammad Fauzi Azmi, Nur Liyana T Technology (General) TA168 Systems engineering Cell culture is undeniably important for multiple scientific applications, including pharmaceuticals, transplants, and cosmetics. However, cell culture involves multiple manual steps, such as regularly analyzing cell images for their health and morphology. Computer scientists have developed algorithms to automate cell imaging analysis, but they are not widely adopted by biologists, especially those lacking an interactive platform. To address the issue, we compile and review existing open-source cell image processing tools that provide interactive interfaces for management and prediction tasks. We highlight the prediction tools that can detect, segment, and track different mammalian cell morphologies across various image modalities and present a comparison of algorithms and unique features of these tools, whether they work locally or in the cloud. This would guide non-experts to determine which is best suited for their purposes and, developers to acknowledge what is worth further expansion. In addition, we provide a general discussion on potential implementations of the tools for a more extensive scope, which guides the reader to not restrict them to prediction tasks only. Finally, we conclude the article by stating new considerations for the development of interactive cell imaging tools and suggesting new directions for future research. PeerJ, Inc. 2023-05-16 Article PeerReviewed application/pdf en http://irep.iium.edu.my/104688/3/104688_A%20review%20of%20open-source.pdf application/pdf en http://irep.iium.edu.my/104688/9/104688_A%20review%20of%20open-source_Scopus.pdf Malik, Hafizi and Idris, Ahmad Syahrin and Toha @ Tohara, Siti Fauziah and Mohd Idris, Izyan and Daud, Muhammad Fauzi and Azmi, Nur Liyana (2023) A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations. PeerJ Computer Science, 9. pp. 1-33. E-ISSN 2376-5992 https://peerj.com/articles/cs-1364/ 10.7717/peerj-cs.1364
institution Universiti Islam Antarabangsa Malaysia
building IIUM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider International Islamic University Malaysia
content_source IIUM Repository (IREP)
url_provider http://irep.iium.edu.my/
language English
English
topic T Technology (General)
TA168 Systems engineering
spellingShingle T Technology (General)
TA168 Systems engineering
Malik, Hafizi
Idris, Ahmad Syahrin
Toha @ Tohara, Siti Fauziah
Mohd Idris, Izyan
Daud, Muhammad Fauzi
Azmi, Nur Liyana
A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations
description Cell culture is undeniably important for multiple scientific applications, including pharmaceuticals, transplants, and cosmetics. However, cell culture involves multiple manual steps, such as regularly analyzing cell images for their health and morphology. Computer scientists have developed algorithms to automate cell imaging analysis, but they are not widely adopted by biologists, especially those lacking an interactive platform. To address the issue, we compile and review existing open-source cell image processing tools that provide interactive interfaces for management and prediction tasks. We highlight the prediction tools that can detect, segment, and track different mammalian cell morphologies across various image modalities and present a comparison of algorithms and unique features of these tools, whether they work locally or in the cloud. This would guide non-experts to determine which is best suited for their purposes and, developers to acknowledge what is worth further expansion. In addition, we provide a general discussion on potential implementations of the tools for a more extensive scope, which guides the reader to not restrict them to prediction tasks only. Finally, we conclude the article by stating new considerations for the development of interactive cell imaging tools and suggesting new directions for future research.
format Article
author Malik, Hafizi
Idris, Ahmad Syahrin
Toha @ Tohara, Siti Fauziah
Mohd Idris, Izyan
Daud, Muhammad Fauzi
Azmi, Nur Liyana
author_facet Malik, Hafizi
Idris, Ahmad Syahrin
Toha @ Tohara, Siti Fauziah
Mohd Idris, Izyan
Daud, Muhammad Fauzi
Azmi, Nur Liyana
author_sort Malik, Hafizi
title A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations
title_short A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations
title_full A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations
title_fullStr A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations
title_full_unstemmed A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations
title_sort review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations
publisher PeerJ, Inc.
publishDate 2023
url http://irep.iium.edu.my/104688/3/104688_A%20review%20of%20open-source.pdf
http://irep.iium.edu.my/104688/9/104688_A%20review%20of%20open-source_Scopus.pdf
http://irep.iium.edu.my/104688/
https://peerj.com/articles/cs-1364/
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score 13.211869

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