LOCI is excited to announce funding from the Chan-Zuckerberg Institute to continue development on our in-house image acquisition software μManager. Funding will provide resources to improve functionality and increase the user base of the program, as well as integrate the μManager platform with LOCI's popular ImageJ image analysis software. Leads on the project will be LOCI's Mark Tsuchida and Bing Dai under principal investigator Kevin Eliceiri with collaboration from Nico Stuurman, University of California - San Francisco.
CZI's Open Source Software Initiative seeks to provide funding to projects in the support of modern scientific research. This year, 32 proposals representing 42 software projects were granted funding.
Find additional details about μManager and CZI here: https://news.wisc.edu/professor-will-make-workhorse-microscope-more-powerful/
When describing the future of microscopy, Jan Huisken imagines an alien landing for the first time on earth, trying to size up the human species.
After seeing a few dozen subjects, the alien might get thrown off by some people wearing glasses, others with long or short hair, or differences in stature. But it will eventually figure out the patterns: This species has two arms and legs, two eyes, a mouth, two ears, etc. It would define the baseline, then focus more on features such as height, gender, pigmentation, eye color, and other interesting traits.
Huisken wants research microscopes capable of doing the same thing.
“In an attempt to understand how diverse development is, we don’t want to image specimens hundreds of times blindly,” says Huisken. “After the first handful, we should figure out what an organism looks like, then go out and find the defining features and the peculiarities that tell us more.”
As the medical engineering lead at Morgridge, Huisken will continue his innovations in “smart microscopy” by building custom devices both for his own lab and for the campus research community. The concept is creating microscopes that are customized, self-learning and to some degree self-directed, being able to separate the meaningful from the mundane.
Huisken invented light sheet microscopy, which captures the sensitive biology of live specimens in an almost entirely unaltered environment. Huisken fielded a few questions recently about smart microscopy and his plans at Morgridge and UW-Madison, where he is a professor of biomedical engineering.
Morgridge and LOCI Postdoctoral Fellow Ellen T. Arena led ImageJ workshops "Introduction and Segmentation" and "Automation and Scripting" at the Wisconsin Institute for Discovery on October 31st and November 1st.
Downloads for instructional materials to complement the courses are available on ImageJ.net and include Image Analysis with Fiji, Segmentation with Fiji, and Scripting with Fiji.
ImageJ is an open source Java image processing program that will run on any computer with a Java 1.6 or later virtual machine. Downloadable distributions are available for Windows, Mac OS X and Linux. FIJI is a distribution of ImageJ with a particular focus on microscopy image analysis. ImageJ and FIJI have a strong, established user base, with thousands of plugins and macros for performing a wide variety of tasks. LOCI is helping lead the development of both ImageJ and FIJI.