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Python image analysis tool reveals the basis of coordinated human kidney function

Nature Reviews Nephrology volume 22, page 5 (2026)Cite this article

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Advances in light sheet fluorescence microscopy (LSFM) and tissue clearing have enabled 3D imaging of intact tissue samples; however, the analytical tools for processing these datasets have lagged behind technological advances in imaging capabilities. To address the analytical gap in 3D image processing, we developed NetTracer3D — an open-source Python tool that converts volumetric imaging data into quantifiable network graphs. Moreover, we have demonstrated the utility of NetTracer3D to ascertain the morphological organization of neurovasculature in LSFM images from thick human kidney tissue slices.

The innervation comprises both sympathetic and sensory fibres that primarily target the juxtaglomerular apparatus while also ensheathing the Bowman’s capsules of each nephron and creating inter-capsular connections avascularly. Critically, we identified neural connectivity between juxtaglomerular apparatuses and downstream nephron segments, with nerve fibres extending from efferent arterioles to the loops of Henle, collecting ducts and proximal tubules in the local vicinity, demonstrating sophisticated synchronization mechanisms. Finally, the insights provided by NetTracer3D demonstrate how these networks change in disease. For example, patients with chronic kidney disease associated with type 2 diabetes demonstrate a broad loss of innervation whereas sclerotic glomeruli from aged patients are over-innervated.

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Acknowledgements

I acknowledge S. Jain, Washington University School of Medicine, for his mentorship.

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  1. Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA

    Liam McLaughlin

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  1. Liam McLaughlin
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Correspondence to Liam McLaughlin.

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The copyright of NetTracer3D is held by Washington University in St. Louis, and L.M. may receive royalties from commercial use.

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McLaughlin, L. Python image analysis tool reveals the basis of coordinated human kidney function. Nat Rev Nephrol 22, 5 (2026). https://doi.org/10.1038/s41581-025-01024-2

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  • DOI: https://doi.org/10.1038/s41581-025-01024-2

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