Hi! I’m Michael S. Nelson.
I study microscopy and image analysis at LOCI, which is a lab located in the building shown here, and is part of the University of Wisconsin - Madison.
In the Image Analysis section, accessible through the menu at the top of the site, is a good amount of information on QuPath workflows and scripting, which is really the main reason this site exists!
In vivo image on Santa Monica beach substrate
Yes. That kind of humor.
Image analysis news!
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Image analysis news! ^__^
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Current Work
I have two primary interests at LOCI (the Eliceiri lab), promoting transparent, open science, and understanding complex biological problems using microscopy, image analysis, and machine learning. My current work is focusing on Python based control software for the Flamingo lightsheet microscope developed by the Huisken lab.
Image Analysis
QuPath - I have been interested in 2D image analysis for the last four years, and strongly support the open and accessible nature of QuPath. In order for this experience to benefit the community, I have created guides in order to help users perform cluster and neighborhood analyses through CytoMAP, and started a blog to help new users get started with scripting.
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.
I have also worked on integrating open source software to control multi-modal microscopes, which allows us to efficiently collect more and more data from what are often limited patient samples.
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!