LimbLab: Pipeline for 3D Analysis and Visualisation of Limb Bud Gene Expression

Abstract

MotivationAlthough 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 efficeint pipeline for staging each data-set, and then aligning and warping the data into a standard atlas for convenient visualisation. ResultsWe 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. Our results highlight the pipelines effectiveness in managing complex 3D gene expression data, enhancing the accuracy and reproducibility of limb development studies. Availability and ImplementationLimbLab is released under the MIT license. The pipeline is implemented in Python and is available as an open-source package. It can be easily installed via pip and is accompanied by comprehensive documentation (https://limblab.embl.es/) to support users at various levels of expertise. The pipeline can be accessed and downloaded at https://github.com/LauAvinyo/limblab.