2025/04/13 by Laura Aviñó-Esteban, Heura Cardona-Blaya, Marco Musy +3 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Congenital heart defects research
paper · pdf · doi:10.1101/2025.04.08.647723
openalex publication_date 2025/04/13 · openalex created_date 2025/04/14 · openalex updated_date 2026/07/14
Abstract Motivation 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 efficeint pipeline for staging each data-set, and then aligning and warping the data into a standard atlas for convenient visualisation. Results 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. Our results highlight the pipeline’s effectiveness in managing complex 3D gene expression data, enhancing the accuracy and reproducibility of limb development studies. Availability and Implementation LimbLab 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 .