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METHODS article

Front. Physiol.
Sec. Computational Physiology and Medicine
Volume 15 - 2024 | doi: 10.3389/fphys.2024.1440099

ColocZStats: A Z-Stack Signal Colocalization Extension Tool for 3D Slicer

Provisionally accepted
Xiang Chen Xiang Chen 1Teena Thakur Teena Thakur 2Anand D. Jeyasekharan Anand D. Jeyasekharan 2Touati Benoukraf Touati Benoukraf 2,3*Oscar Meruvia-Pastor Oscar Meruvia-Pastor 4*
  • 1 Department of Computer Science, Faculty of Science, Memorial University of Newfoundland, John's, Newfoundland and Labrador, Canada
  • 2 Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
  • 3 Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
  • 4 Memorial University of Newfoundland, St. John's, Canada

The final, formatted version of the article will be published soon.

    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 relationship between different molecules. In addition, despite the established advantages and growing adoption of 3D visualization software in various microscopy research domains, there has been a scarcity of systems supporting colocalization analysis within a user-specified region of interest (ROI). 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 threedimensional (3D) reconstructions for the z-stacks and in some cases transfer them into an immersive Virtual Reality (VR) scene, there is still a lack of 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 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.

    Keywords: confocal microscopy, Colocalization analysis, Confocal microscopy visualization, 3D Slicer, Virtual reality (VR), volume rendering

    Received: 29 May 2024; Accepted: 12 Aug 2024.

    Copyright: © 2024 Chen, Thakur, Jeyasekharan, Benoukraf and Meruvia-Pastor. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Touati Benoukraf, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, A1C 5R3, Newfoundland and Labrador, Canada
    Oscar Meruvia-Pastor, Memorial University of Newfoundland, St. John's, Canada

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.