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Kinetochore tracking in 3D from lattice light sheet imaging data with KiT
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Harrison, Jonathan, Sen, Onur, McAinsh, Andrew D. and Burroughs, Nigel John (2022) Kinetochore tracking in 3D from lattice light sheet imaging data with KiT. Bioinformatics, 38 (12). pp. 3315-3317. doi:10.1093/bioinformatics/btac330 ISSN 1460-2059.
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WRAP-Kinetochore-tracking-3D-lattice-light-sheet-imaging-data-KiT-2022.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (404Kb) | Preview |
Official URL: https://doi.org/10.1093/bioinformatics/btac330
Abstract
Motivation:
Lattice light sheet microscopy is revolutionizing cell biology since it enables fast, high-resolution extended imaging in three dimensions combined with a drastic reduction in photo-toxicity and bleaching. However analysis of such data sets still remains a major challenge.
Results:
Automated tracking of kinetochores, the protein complex facilitating and controlling microtubule attachment of the chromosomes within the mitotic spindle, provides quantitative assessment of chromosome dynamics in mitosis. Here we extend existing open-source kinetochore tracking software (KiT Armond et al. [2016]) to track (and pair) kinetochores throughout pro-metaphase to anaphase in lattice light sheet microscopy data. One of the key improvements is a regularization term in the objective function to enforce biological information about the number of kinetochores in a human mitotic cell, as well as improved diagnostic tools. This software provides quantitative insights into how kinetochores robustly ensure congression and segregation of chromosomes during mitosis.
Availability and implementation:
KiT is free, open-source software implemented in MATLAB and can be downloaded as a package from https://github.com/cmcb-warwick/KiT. The source repository is available at https://bitbucket.org/jarmond/kit (tag v2.4.0) and under continuing development.
Supplementary information:
Supplementary data are available at Bioinformatics online.
| Item Type: | Journal Article | ||||||||||||
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| Subjects: | Q Science > QH Natural history Q Science > QP Physiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Mathematics Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| SWORD Depositor: | Library Publications Router | ||||||||||||
| Library of Congress Subject Headings (LCSH): | Fluorescence microscopy -- Data processing, Enzymes -- Analysis, Chromosomes, Cell organelles, Mitosis | ||||||||||||
| Journal or Publication Title: | Bioinformatics | ||||||||||||
| Publisher: | Oxford University Press (OUP) | ||||||||||||
| ISSN: | 1460-2059 | ||||||||||||
| Official Date: | 15 June 2022 | ||||||||||||
| Dates: |
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| Volume: | 38 | ||||||||||||
| Number: | 12 | ||||||||||||
| Page Range: | pp. 3315-3317 | ||||||||||||
| DOI: | 10.1093/bioinformatics/btac330 | ||||||||||||
| Status: | Peer Reviewed | ||||||||||||
| Publication Status: | Published | ||||||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||
| Date of first compliant deposit: | 27 June 2022 | ||||||||||||
| Date of first compliant Open Access: | 27 June 2022 | ||||||||||||
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