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.
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.”
Play us a song: the (Hyper)piano man
Christopher Taylor has the hands of a musician, his fingers most at home striking the keys of a piano, and an analytical mind honed by years of computer programming. Now after tackling his latest endeavor, Taylor can also call himself an engineer, a builder, a maker.
Taylor, a professor in the School of Music at UW-Madison, recently finished building a Hyperpiano– an instrument of his own design– in the Fab Lab of the Medical Engineering theme at the Morgridge Institute for Research. The master instrument has two keyboards that outsource sound by wirelessly sending signals to two secondary pianos.
“I’d never done any woodworking before, and certainly nothing in the machine shop,” Taylor says. “Going into this project, I barely knew the different sizes of screws. But designing and creating has been very satisfying, and I’ve enjoyed learning all these new skills.”
Kevin Eliceiri, director of the Fab Lab, says it was Taylor’s unique vision and passion for the project that made him and his piano a good fit for the Fab Lab.
Read the story at the Morgridge Institute for Research News . . .
Andreas Velten wins major imaging award
The Society for Imaging Science and Technology (IS&T) and Image Engineering GmbH & Co. KG are pleased to announce that the 2016 Image Engineering Innovation Award (IEIA) is given to Andreas Velten, University of Wisconsin-Madison, “for the development of a time-of-flight, ultra-fast photography system.”
Andreas Velten leads the Computational Optics Group at the Laboratory for Optical and Computational Instrumentation (LOCI) at UW-Madison. He is a fellow of the Wisconsin Institute for Discovery, a member of the UW Living Environments Lab, and an affiliate of the Medical Engineering Group at the Morgridge Institute for Research in Madison.
He also is the co-founder of two active startup companies: OnLume, a medical device company, and Formula Database, an online learning platform.
Read the story at Morgridge Institute for Research News . . .
UW-Madison and Morgridge researchers associate collagen architecture with glioblastoma patient survival
A new report in the Journal of Neurosurgery, "Association of collagen architecture with glioblastoma patient survival" by University of Wisconsin-Madison investigators Kelli Pointer, Cellular and Molecular Biology Graduate Program in the laboratory of John Kuo, Department of Neurological Surgery and Kevin Eliceiri, Laboratory of Optical and Computational Instrumentation (LOCI) as well as Alex Schroeder, Medical Physics Graduate Program, LOCI, and the Morgridge Institute for Research shows a correlation between collagen and glioblastoma progression. The group was the first to visualize collagen architecture in glioblastoma using the Optical Workstation at LOCI: a multiphoton laser scanning system with second harmonic generation (SHG) imaging capabilities. The group showed that glioblastoma can be visualized by SHG and collagen alignment can be correlated with tumor invasiveness and patient survival.