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Automated Image Processing Workflow for Morphological Analysis of Fluorescence Microscopy Cell Images

Voigt, SP and Ravikumar, K and Basu, B and Kalidindi, SR (2021) Automated Image Processing Workflow for Morphological Analysis of Fluorescence Microscopy Cell Images. In: JOM, 73 . pp. 2356-2365.

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Official URL: https://doi.org/10.1007/s11837-021-04707-w


Computerized image analysis of biological cells and tissues is a necessary complement to high-throughput microscopy, allowing researchers to effectively analyze large volumes of cellular data. It has the potential to dramatically improve the throughput and accuracy of measurements and related downstream analyses that may be obtained from images. This study presents a novel workflow for automated analysis of fluorescence microscopy images, which benefits from running multiple segmentation workflows and combining them to produce the best final segmentation. It is tested using a dataset of 42 fluorescence microscopy cells, evaluated against a hand segmented dataset using the F1 score, and critically compared to a single segmentation workflow, which served as a control. The accuracy and reliability of the novel workflow are demonstrated to be superior to the control workflow, which achieved F1 scores of 0.845 and 0.608, respectively. The workflow and example code are available through an open-source software platform. © 2021, The Minerals, Metals & Materials Society.

Item Type: Journal Article
Publication: JOM
Publisher: Springer
Additional Information: The copyright for this article belongs to Springer
Keywords: Fluorescence; Fluorescence microscopy; Image enhancement; Image segmentation; Open source software; Open systems, Accuracy of measurements; Automated analysis; Automated image processing; Biological cells; Fluorescence microscopy images; High throughput; Morphological analysis; Multiple segmentation, Image analysis
Department/Centre: Division of Chemical Sciences > Materials Research Centre
Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering
Date Deposited: 04 Aug 2021 10:47
Last Modified: 04 Aug 2021 10:47
URI: http://eprints.iisc.ac.in/id/eprint/69072

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