LOCI's μManager 2.0 Receives Support from CZI

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/

Jan Huisken: Building a better, smarter microscope

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.

Read the story at Morgridge Institute for Research News & Stories . . .


David Parkins ©2015 Nature America

ImageJ Introduction and Segmentation, Automation and Scripting with Ellen Arena

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

Morgridge and LOCI Postdoctoral Fellow Ellen T. Arena leads ImageJ workshops "Introduction and Segmentation" and "Automation and Scripting" at the Wisconsin Institute for Discovery on October 31st and November 1st.

Study links changes in collagen to worse pancreatic cancer prognosis

A study in the current journal Oncotarget provides the first evidence linking a disturbance of the most common protein in the body with a poor outcome in pancreatic cancer.

The study reinforces growing evidence that collagen, which forms fibrous networks in skin, tendons and muscles, is intimately involved in several cancers, says the paper’s corresponding author, Kevin Eliceiri, director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin–Madison.

For the study, the Wisconsin researchers examined surgical tissues from 114 pancreatic cancer patients and identified a particular rearrangement of collagen fibers surrounding the tumor as a “biomarker” of early death.

A similar rearrangement of collagen has also been found in breast cancer, head, neck, esophageal and colorectal cancers.

“Collagen is the most abundant protein in the body,” says Eliceiri. “It’s a beautiful molecule — wavy, with a fibrous nature. Without it we would be a sack of nothing. With this little molecule, the specific fiber organization really matters to metastasis.”

The images were created using an automated laser scanning microscope developed at LOCI that shines a laser at tumor specimens mounted on microscope slides. The laser’s bright, rapid pulses interact with the collagen fibers, which glow and reveal exquisite details of their structure and relationship to nearby fibers.

The new study tested how collagen formation might affect metastasis, Eliceiri says. “We did not know anything about survival when we measured the alignment of the collagen in tumors from 114 pancreatic cancer patients. When we looked at the clinical records, we found that the tumors with highly aligned collagen fibers had the worst survival. To our knowledge, this is the first time this technique was used for prognostic purposes in pancreatic cancer.”

First author Cole Drifka, a biomedical engineering postdoctoral researcher, conceived and performed the study under the supervision of Eliceiri and W. John Kao, a professor of pharmacy. “The powerful tissue resource used in this study was made possible by generous financial donations from Teresa’s Foundation for Pancreatic Cancer and the Tim and Mary Ann McKenzie Chair of Surgical Oncology Professorship,” says Drifka. “Above all, it was made possible by the selfless tissue donations by UW Health patients. The new tissue collection represents a blossoming institutional focus on pancreatic cancer and is now available to all campus researchers seeking to comprehend this challenging disease.”

Read the story at UW News . . .