Chen, Xiang (2024) ColocZStats: a 3D Slicer extension for assessing colocalization in confocal microscopy. Masters thesis, Memorial University of Newfoundland.
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Abstract
Confocal microscopy has evolved as a widely adopted imaging technique in molecular biology and is frequently utilized to achieve accurate subcellular localization of proteins. Applying colocalization analysis on image z-stacks obtained from confocal fluorescence microscopes is a dependable method to reveal the association between different molecules. In addition, despite the established advantages and growing adoption of virtual reality (VR) technology in various microscopy research domains, there has been a scarcity of systems supporting colocalization analysis within VR space. In this context, several broadly employed biological image visualization platforms were meticulously explored in this study to comprehend the current landscape. It has been observed that while these applications can generate three-dimensional (3D) reconstructions for the z-stacks and transfer them into an immersive VR scene, there is still a common necessity for them to optimize the capability for executing quantitative colocalization analysis on such images. To constructively improve the above circumstances, an extension called ColocZStats has been developed for 3D Slicer. With a user-friendly interface, ColocZStats allows investigators to conduct intensity thresholding and region-of-interest (ROI) selection on imported 3D image stacks. It can deliver several essential colocalization metrics for structures of interest in the form of diagrams and spreadsheets. While currently serving as a desktop tool, ColocZStats has been continuously enhanced and will be systematically extended into VR in the next phase.
| Item Type: | Thesis (Masters) |
|---|---|
| URI: | http://research.library.mun.ca/id/eprint/16522 |
| Item ID: | 16522 |
| Additional Information: | Includes bibliographical references (pages 58-76) -- Restricted until March 18, 2024 |
| Keywords: | confocal microscopy, colocalization analysis, confocal microscopy visualization, 3D Slicer, virtual reality (VR) |
| Department(s): | Science, Faculty of > Computer Science |
| Date: | June 2024 |
| Date Type: | Submission |
| Library of Congress Subject Heading: | Confocal microscopy; Virtual reality; Image analysis |
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