# Limblab: pipeline for 3D analysis and visualisation of limb bud gene expression

## TL;DR

Limblab is a new pipeline for 3D analysis and visualization of limb bud gene expression patterns during development.

## Contribution

The paper introduces a modular, user-friendly pipeline for 3D analysis of limb development gene expression data.

## Key findings

- The pipeline integrates data acquisition, cleaning, staging, alignment, and visualization for 3D limb bud analysis.
- It is compatible with tools like Fiji and Vedo, and can be customized for different research workflows.
- The pipeline is scalable and optimized for future expansion to other species and developmental fields.

## Abstract

Although some aspects of limb development can be treated as a 2D problem, a true understanding of the morphogenesis and patterning requires 3D analysis. Since the data on gene expression patterns are largely static 3D image stacks, a major challenge is an efficient pipeline for staging each data-set, and then aligning and warping the data into a standard atlas for convenient visualisation.

We present a novel bioinformatic pipeline tailored for 3D visualization and analysis of developing limb buds. The pipeline integrates key steps such as data acquisition, volume cleaning, surface extraction, staging, alignment, and advanced visualization techniques. Its modular design allows researchers to customize workflows while maintaining compatibility with tools such as Fiji and Vedo. The pipeline can be accessed at https://github.com/LauAvinyo/limblab.

The pipeline advances 3D gene expression analysis in limb development by integrating flexible tools for staging, alignment, and visualization. It is user-friendly, scalable to other samples, and optimized for research needs. Future updates will enhance customization and expand applicability to other species and developmental biology fields.