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Updated: Jan 11, 2026

Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution

Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution

Published on: June 6, 2019

Ce -NeRV3D - a C. elegans Neuron RNA-seq Visualization tool in 3D.

Luca Golinelli¹, Majdulin Nabil Istiban¹, Jan Watteyne¹

¹Department of Biology, KU Leuven, Leuven, Flanders, Belgium.

Micropublication Biology

|November 10, 2025

Summary

This summary is machine-generated.

We developed Ce-NeRV3D, a tool for visualizing gene expression in the C. elegans nervous system. This 3D visualization helps researchers explore transcriptomic data within detailed neural anatomy.

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Area of Science:

Neuroscience
Computational Biology
Genomics

Background:

Caenorhabditis elegans is a model organism with a fully mapped connectome and single-cell transcriptomic data.
Understanding gene expression within neural circuits is crucial for studying brain function.

Purpose of the Study:

To present Ce-NeRV3D, a novel 3D visualization tool for C. elegans neural transcriptomics.
To enable interactive exploration of gene expression patterns within the worm's nervous system.

Main Methods:

Developed Ce-NeRV3D as a Blender plug-in.
Integrated C. elegans neural anatomy with single-cell RNA sequencing data.
Implemented customizable color mapping for gene co-expression visualization.

Main Results:

Ce-NeRV3D allows visualization of unlimited gene expression patterns in 3D.
Users can overlay transcriptomic data onto the worm's neural structure.
The tool facilitates interactive examination of gene expression in anatomical context.

Conclusions:

Ce-NeRV3D enhances the study of neural circuits by integrating transcriptomics and neuroanatomy.
This tool provides a powerful platform for exploring spatial gene expression in C. elegans.
Facilitates discovery in neurobiology through advanced data visualization.