Hi! I’m Michael S. Nelson.
I'm a PhD candidate in Biomedical Engineering at the University of Wisconsin–Madison, working in the Eliceiri lab (LOCI). I build microscope control software and study collagen structure in the tumor microenvironment using light sheet and polarization microscopy.
This site focuses on QuPath workflows and scripting—tutorials, guides, and resources for the image analysis community.
In vivo image on Santa Monica beach substrate
Yes. That kind of humor.
Current Work
My research focuses on two main projects: (1) Python-based control software for light sheet microscopy, enabling 3D imaging of collagen networks in cleared tissue, and (2) QuPath-based control software for polychromatic polarization microscopy, designed for integration into clinical pathology workflows.
I'm also active in open science initiatives: a steering committee member for QUAREP-LiMi, administrator on the Image.sc forum, and a founding member of BINA's Early Career working group.
Image Analysis
I've worked with QuPath since 2017 and have contributed scripts, tutorials, and workflow guides to help the community get the most out of this open-source platform. Resources here include multiplex analysis workflows, CytoMAP integration for cluster and neighborhood analysis, and scripting tutorials for users at all levels.
I also collaborated with Johanna M. Dela Cruz on a video tutorial series for multiplex analysis.
Microscopy
An Image is Worth 1,000 Words
But what if we make a movie?
Microscopy data can provide a wealth of information about systems by recording both the temporal and spatial information related to the samples analyzed.
My microscopy experience spans widefield, confocal, two-photon, light sheet, and whole slide scanning—both operating instruments and building control software. At City of Hope's Light Microscopy Core, I trained researchers and supported experiments from simple scratch assays to multi-day live imaging of embryonic tissue.
Current work: developing open-source control software for light sheet and polarization microscopy systems, with a focus on bridging research imaging and clinical pathology.
Video courtesy of Dr. Nadia Carlesso and Christina Abundis.
About Me
Find out more about my experience and education, or just drop me a line!