Scholarlink

Background <p>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.</p> Results <p>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 <a href="https://github.com/LauAvinyo/limblab">https://github.com/LauAvinyo/limblab</a>.</p> Conclusions <p>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.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年1月12日

查看全文
  • Laura Aviñó-Esteban,
  • Heura Cardona-Blaya,
  • Marco Musy,
  • Antoni Matyjaszkiewicz,
  • James Sharpe,
  • Giovanni Dalmasso

摘要

Background

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.

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. The pipeline can be accessed at https://github.com/LauAvinyo/limblab.

Conclusions

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.