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Author Spotlight: In Vivo Whole-Brain Imaging of Zebrafish Larvae Using Three-Dimensional Fluorescence Microscopy
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ZF-Mapper: Simple and Complete Freeware for Fluorescence Quantification in Zebrafish Images
Daiki Yamamoto1, Daisuke Sato2, Hiroko Nakayama3,4
11 Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Japan.
Zebrafish
|March 12, 2019
Summary
ZF-Mapper is a new open-source software tool for quantifying fluorescence in zebrafish images. This Python-based freeware simplifies fluorescence-based screening and provides results comparable to existing methods.
Area of Science:
- Developmental Biology
- Bioimaging
- Computational Biology
Background:
- Zebrafish are transparent vertebrate models ideal for live imaging.
- Existing fluorescence quantification software is complex and lacks open-source code.
- Need for accessible tools for analyzing fluorescent signals in zebrafish.
Purpose of the Study:
- To develop a simple, robust, open-source software tool for zebrafish fluorescence quantification.
- To enable efficient batch processing and 3D analysis of fluorescence intensity.
- To facilitate fluorescence-based screening in zebrafish research.
Main Methods:
- Developed ZF-Mapper, a Python-based open-source software.
- Implemented pixel-level fluorescence intensity quantification.
- Enabled batch processing of multiple zebrafish images.
- Validated results against ImageJ and applied to cancer xenografts.
- Integrated with R freeware for interactive 3D visualization.
Main Results:
- ZF-Mapper accurately quantifies fluorescence intensity in zebrafish.
- Results are equivalent to conventional software like ImageJ.
- Successfully quantified macrophage-specific EGFP and tdTomato-labeled melanoma cells.
- Enabled interactive 3D scatter plots of fluorescence data.
Conclusions:
- ZF-Mapper is a user-friendly, open-source tool for zebrafish fluorescence analysis.
- The software supports batch processing and 3D visualization.
- ZF-Mapper facilitates efficient fluorescence-based screening in zebrafish models.
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