My name is Michael Nelson, and I'm a PhD candidate in Biomedical Engineering at the University of Wisconsin–Madison, building microscope control software and studying collagen in the tumor microenvironment.
Background
Michael, leaning against a fence above the California coastline. Photo courtesy of Diana Simons.
I grew up on the east coast, in central Virginia—so I had the chance to experience "weather" before moving to southern California for college at Harvey Mudd (chemistry) and my master's work at The Scripps Research Institute (crystallography). After a decade in IT, I transitioned into image analysis and, with the help of Brian Armstrong at City of Hope, microscopy. At City of Hope's Light Microscopy Core, I trained researchers, supported experiments from scratch assays to multi-day live imaging, and developed analysis pipelines—work I've continued collaborating on through 2025.
I'm now in my final year of a PhD in Biomedical Engineering at UW-Madison, where I'm building open-source control software for light sheet and polarization microscopy systems. My goal is to tie together my background in coding, chemistry, and biological imaging to build tools that help scientists navigate complex imaging infrastructure more effectively.
And yes, I've had to relearn how to deal with weather. Current temperature as I type, a balmy -15C.
Open science is the key to the future
I operate at the intersection of image analysis, coding, biology, and microscopy. My introduction to image analysis came through QuPath and the amazing support provided by its author, Pete Bankhead. My continued experiences with both open and proprietary software, and the companies and groups that produce them, have led me to the conclusion that the way forward is truly open solutions where everyone is free to understand how the code works. Creating open solutions that are not only transparent but also easy to use is a lot of work, however. Implementing these solutions will require international collaborations and financial support. Several companies including RareCyte and ACDbio are looking into the use of QuPath to support their other products.
Openness and transparency go beyond "free" software, allowing different open programs to integrate into pipelines where each step of the process can be dissected and understood. Such pipelines will also increase the re-usability of scientific articles and the repeatability of results - speeding overall scientific progress and eliminating dead ends due to poorly chosen scientific experimental designs. I serve on the steering committee for QUAREP-LiMi, a worldwide initiative to improve quality and reproducibility in light microscopy. I'm also an administrator on the Image.sc forum, a founding member of BINA's Early Career working group, and taught image analysis at MBL's Analytical and Quantitative Light Microscopy course in 2023.
Member of:
LOCI: Laboratory of Kevin Eliceiri at UW-Madison
QUAREP-LiMi: Steering committee member — a worldwide initiative focused on light microscopy quality and reproducibility
Image.sc Forum: Administrator — the central hub for open-source bioimage analysis discussion
BINA: Founding member, Early Career working group
JEDI: Joint Effort to Develop multiplex Immunofluorescence standards, a SITC multiplex analysis focus group
Webinar on multiplex image analysis hosted by Akoya
Download slides from webinar
Other (non-QuPath) open source projects and collaborations I support/follow.
COBA: Center for Open Bioimage Analysis
A collaboration between the Broad Institute and UW-Madison.
FIJI
FIJI is a continuation of the open source development of image analysis software that started with NIH Image, followed by ImageJ at the NIH.
Image.SC Forum
The central forum for open-source bioimage analysis discussion. I serve as an administrator, helping maintain this community resource for researchers worldwide.
Micro Manager
Open-source microscope control software - now controllable through PycroManager to allow control through Python scripting.
Contact Me
If you can’t find me in the lab, send me an email!
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