High-throughput, organ-scale 3D tubule tracking using TubuleMAP

Area of Science:

• Biomedical Imaging
• Computational Biology
• Histology

Background:

• Mesoscale imaging of intact tubular networks is advancing with tissue clearing and lightsheet microscopy.
• Analytical tools for 3D tubule mapping, continuity assessment, and injury pattern analysis are currently limited.

Purpose of the Study:

• To develop a semi-automated pipeline, TubuleMAP, for 3D tubule tracking and reconstruction.
• To enable large-scale analysis of complex tubular networks with high throughput and reduced human effort.

Main Methods:

• TubuleMAP is a semi-automated pipeline utilizing parallel processing for terabyte-scale data.
• It adapts to diverse morphological and staining patterns and includes a napari interface for human oversight.
• The pipeline performs 3D tubule tracking and reconstruction.

Main Results:

• Reconstructed 1,000 intact mouse nephrons from ~1-millimeter-thick kidney tissue with ~400-fold higher throughput and <1% human effort.
• Demonstrated generalizability by reconstructing all seminiferous tubules in a mouse testis within a day.
• Enabled mesoscale nephron organization analysis, quantitative profiling of pathologies, and whole-nephron cytometry.

Conclusions:

• TubuleMAP provides a powerful tool for analyzing complex tubular structures at unprecedented scales.
• The open-source pipeline facilitates detailed investigation of tissue architecture and pathology.
• This technology advances the study of tubular networks in various biological contexts.