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Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

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DEVILS: a tool for the visualization of large datasets with a high dynamic range.

Romain Guiet¹, Olivier Burri¹, Nicolas Chiaruttini¹

¹BioImaging & Optics platform (BIOP), Faculty of Life Sciences (SV), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

|May 14, 2021

Summary

A new ImageJ plugin, DEVILS, enhances visualization of large image datasets by homogenizing intensities. This allows simultaneous viewing of dim and bright structures, overcoming display limitations for better analysis.

Keywords:

BigDataViewer Image Processing ImageJ/Fiji Large datasets Light-sheet fluorescence microscopy

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Area of Science:

Microscopy and Image Analysis
Computational Biology
Bioimaging

Background:

Limited displayable grey values challenge visualization of large dynamic range image data.
Difficulty in observing both dim and bright structures simultaneously, especially with intensity variations.
Existing simple intensity mappings fail to provide comprehensive visualization in a single view.

Purpose of the Study:

To develop an ImageJ plugin for compressed display of features across multiple intensity magnitudes.
To enable simultaneous visualization of high and low intensity features in large volumetric datasets.
To facilitate easier visualization-based analysis of complex image data.

Main Methods:

Development of the Display Enhancement for Visual Inspection of Large Stacks (DEVILS) ImageJ plugin.
Utilizing a combination of local and global pixel operations for intensity homogenization.
Incorporating a single intuitive parameter, preview mode, and parallelization for efficient processing.

Main Results:

DEVILS plugin successfully homogenizes intensities, making both high and low intensity features visible.
The plugin processes multiple image planes efficiently using parallelization.
Output is compatible with BigDataViewer for rapid visualization of processed datasets.

Conclusions:

The DEVILS plugin offers an easy-to-use solution for visualizing large volumetric image data with wide intensity ranges.
It overcomes limitations of standard display methods, improving the analysis of challenging specimens.
The plugin enhances the visibility of structures with varying intensities, aiding scientific discovery.