Poudel Lab

The Poudel Lab develops advanced tissue processing workflows, high-resolution 3D imaging platforms and computational tools — including machine learning and artificial intelligence — to advance the emerging field of 3D digital pathology. Using these innovative tools, our mission is to enhance the understanding, diagnosis and treatment of disease with the goal of improving human health.

We are deeply committed to collaborative science, working closely with clinical researchers, pathologists and bioengineers to ensure our discoveries are both scientifically robust and translationally meaningful. By bridging basic research with clinical application, we strive to accelerate the development of next-generation diagnostic tools and therapeutic strategies that improve patient outcomes.

Principal Investigator

Chetan Poudel, PhD

Assistant Professor of Medicine

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Research

Distribution of blood vessels and glomeruli in a mouse kidney stained with CD31 antibody. The color encodes depth in this 2D projection.

3D kidney atlases via high-resolution imaging

Our lab is building detailed 3D reference maps of the kidney using advanced imaging modalities such as open-top light-sheet (OTLS) and two-photon microscopy to achieve subcellular resolution across large tissue volumes. To handle the vast and complex datasets generated by 3D microscopy, we have developed custom AI-driven image analysis pipelines, including tailored deep learning models for automated segmentation and tubule tracking. These tools allow us to map the spatial organization of key kidney structure — glomeruli, nephron segments, vasculature, lymphatics and nerves — within intact tissue volumes.

Aims of this project include:

Building comprehensive 3D reference atlases for healthy, acutely injured and chronically diseased kidneys.
Investigating nephron-vascular interactions and their role in kidney disease progression.
Conducting comparative studies between mouse and human kidneys to reveal species-specific anatomical features and inform translational disease modeling and treatment.

3D digital Pathology of Human Kidney Biopsies

Our lab aims to advance 3D digital pathology of human kidney biopsies by combining fluorescent analogs of classical histology stains with high-resolution 3D imaging. This approach enables visualization of entire core needle biopsies and nephrectomy samples in their intact, unsectioned state. Using AI-based analysis tools, we will assess tissue architecture and pathology in full volumetric context, preserving the native 3D relationships between structures such as tubules, vasculature and interstitial compartments.

We aim to demonstrate that 3D digital pathology provides significant advantages over traditional 2D slide-based histopathology, including:

Increased tissue sampling through full-volume imaging.
True 3D visualization of complex anatomical structures.
Reversible, non-destructive workflows that preserve tissue for downstream assays.

This direction represents a paradigm shift in renal pathology, offering greater diagnostic depth while maintaining the integrity of precious clinical samples.

imaging shows glomeruli in a renal biopsy

Automated detection of glomeruli in a patient renal biopsy, stained with a fluorescent PAS analog and imaged with open-top lightsheet microscopy.

Contact Us

The Poudel Lab is looking for exciting collaborations and enthusiastic post-doctoral fellows, graduate students and undergraduate students interested in research at the intersection of engineering and medicine. Please contact Chetan Poudel, PhD, by email.

Postdoctoral or medical (MD/PhD) fellows: If you are interested in our research, have a strong publication record and are highly motivated to make exciting discoveries, please contact us by email. Include your CV and a brief description of research directions you may be most interested in pursuing in our lab.
Graduate students: If you are an Indiana University or Purdue University graduate student looking for rotation possibilities, please contact us by email. Pre-doctoral students can find information about Purdue University's biomedical engineering program.
Undergraduates: If our research interests you, and you would like to inquire about research experience in our lab during the summer or academic year, please contact us.