ColocZStats: a z-stack signal colocalization extension tool for 3D slicer Article Swipe
Xiang Chen
,
Teena Thakur
,
Anand D. Jeyasekharan
,
Touati Benoukraf
,
Oscar Meruvia-Pastor
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3389/fphys.2024.1440099
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3389/fphys.2024.1440099
Confocal microscopy has evolved to be 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 of revealing the relationship between different molecules. In addition, despite the established advantages and growing adoption of 3D visualization software in various microscopy research domains, there have been few systems that can support colocalization analysis within a user-specified region of interest (ROI). In this context, several broadly employed biological image visualization platforms are meticulously explored in this study to understand the current landscape. It has been observed that while these applications can generate three-dimensional (3D) reconstructions for z-stacks, and in some cases transfer them into an immersive virtual reality (VR) scene, there is still little support for performing quantitative colocalization analysis on such images based on a user-defined ROI and thresholding levels. To address these issues, an extension called ColocZStats (pronounced Coloc-Zee-Stats) has been developed for 3D Slicer, a widely used free and open-source software package for image analysis and scientific visualization. With a custom-designed user-friendly interface, ColocZStats allows investigators to conduct intensity thresholding and ROI selection on imported 3D image stacks. It can deliver several essential colocalization metrics for structures of interest and produce reports in the form of diagrams and spreadsheets.
Related Topics
Concepts
Colocalization
Visualization
Thresholding
Computer science
Software
Context (archaeology)
Confocal
Interface (matter)
Artificial intelligence
Computer vision
Graphical user interface
Region of interest
Pattern recognition (psychology)
Image (mathematics)
Biology
Physics
Optics
Paleontology
Parallel computing
Bubble
Maximum bubble pressure method
Programming language
Cell biology
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fphys.2024.1440099
- OA Status
- gold
- References
- 54
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4402245651
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4402245651Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3389/fphys.2024.1440099Digital Object Identifier
- Title
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ColocZStats: a z-stack signal colocalization extension tool for 3D slicerWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
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2024-09-04Full publication date if available
- Authors
-
Xiang Chen, Teena Thakur, Anand D. Jeyasekharan, Touati Benoukraf, Oscar Meruvia-PastorList of authors in order
- Landing page
-
https://doi.org/10.3389/fphys.2024.1440099Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.3389/fphys.2024.1440099Direct OA link when available
- Concepts
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Colocalization, Visualization, Thresholding, Computer science, Software, Context (archaeology), Confocal, Interface (matter), Artificial intelligence, Computer vision, Graphical user interface, Region of interest, Pattern recognition (psychology), Image (mathematics), Biology, Physics, Optics, Paleontology, Parallel computing, Bubble, Maximum bubble pressure method, Programming language, Cell biologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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54Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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