UD interactive conference highlights diagnostic, research benefits of digital pathology

October 3, 2012 under CANR News

With researchers from throughout the world collaborating on projects, the need to share and analyze tissue specimens remotely in real-time is ever present. To preview technology which can help meet that need, the University of Delaware College of Agriculture and Natural Resources’ Comparative Pathology Laboratory hosted “Introduction to Digital Pathology” demonstrations Sept. 6-7 at the Charles C. Allen Laboratory Conference Room.

Conference participants experienced digital pathology, or ePathology, technology firsthand through live demonstrations of slide scanning quantitative image analysis and real-time conferencing on virtual slides without a microscope.

Erin Brannick, assistant professor in the Department of Animal and Food Sciences, director of the CANR Comparative Pathology Laboratory and a veterinary pathologist, organized the conference with representatives from Aperio, a company specializing in digital pathology slide scanners, analysis software, and data management systems.

Digital pathology systems have many applications, and Brannick explained that during the sessions, participants were able to see how one Aperio system could meet the diverse needs of researchers, diagnosticians in human and veterinary medicine, educators and industry partners.

Multiple research application sessions offered individual researchers the chance to create and analyze virtual slides of their own research specimens. The bovine hoof and rumen, marine animal eyes and fungal organisms were among the images scanned on-site for attendees by a machine that can accommodate up to 400 glass slides at a time. Participants could then observe the virtual tissues across magnifications from a whole slide view up to 40x magnification, either on the attached monitor or on one of several laptop computers in the room.

Aperio representatives also demonstrated specific features of Genie, image analysis software that can be trained to meet the individual needs of a user. Once trained, a Genie analysis template can be applied to all virtual slides in a research study simultaneously, minimizing viewer subjectivity and lengthy time requirements typical for manual slide review by an individual researcher.

On the morning of Thursday, Sept. 6, a diagnostic applications conference was held in which diagnosticians from the UD Allen and CANR Comparative Pathology laboratories on Newark campus were able to interface with veterinary diagnosticians from Delaware and Maryland at the Lasher Laboratory in Georgetown, Del., as they held their monthly diagnostic conference. The ability to connect via computer to examine the same slides remotely in real-time is a function that Brannick said could be very beneficial to both diagnosticians and researchers. “Because our groups are so spread apart, it would be nice if we were to get this system on board to be able to conference directly using virtual slides,” she said.

The groups briefly learned about the digital pathology equipment through a standard videoconference, then held a consultation on their diagnostic cases using remotely-linked computers and digital slide images that had been uploaded to Aperio’s servers in California. “I was able to share cases remotely and show participants directly what the lesions were and what I was seeing that helped me make my diagnosis,” said Brannick.

Participants at both locations could take turns analyzing disease lesions at multiple magnifications while discussing details of the case. “We could give Lasher laboratory participants control and they could drive the slide and ask questions,” she said. Despite streaming data from servers across the country, the images uploaded with minimal delay, projected crisply, and maneuvered easily, even for first-time system users.

The diagnostic applications conference was also a first for the Aperio representatives. While remote slide conferencing is a common use for the Aperio imaging system, the UD conference marked the first time the representatives were able to fully demonstrate the intuitive ease of digital conferencing before actually installing a system at a university. “The representatives tell people how to set remote conferencing up all the time but to actually get to do it too was a lot of fun for them,” said Brannick.

As for a teaching tool, Brannick brought the undergraduate and graduate students in her animal histology class in to try the Aperio system to demonstrate to other educators in attendance how beneficial it can be when an entire class can look at the exact same specimen on computer screens as opposed to a variety of samples under individual microscopes.

“If you were to use digital pathology in a lab setting, you could actually have a computer lab where everyone gets the same electronic slide set and then students pull up image after image. You can directly talk with students and guide them as a class through an image,” said Brannick. “Then you could turn control over to the students and have them drive around and show others what they’re looking at and what they see. So that’s a real strength of this system.”

Brannick is now looking to move forward, trying to bring the Aperio brightfield and/or fluorescence digital imaging system to UD on a full-time basis. “We really feel like it will greatly benefit all of these aspects for UD: the research, the teaching and the diagnostics.”

For more information about the Aperio digital pathology technology, contact Erin Brannick at 831-1342.

Article by Adam Thomas

This article can also be viewed on UDaily.


Comparative Pathology Laboratory to host ‘Introduction to Digital Pathology’

August 29, 2012 under CANR News

The University of Delaware College of Agriculture and Natural Resources’ Comparative Pathology Laboratory will host  “Introduction to Digital Pathology” demonstration sessions on Thursday, Sept. 6, and Friday, Sept. 7.

The sessions will be held in the conference room of the Charles C. Allen Laboratory on the UD campus in Newark.

Times and topics are as follows:

Thursday, Sept. 6

8 a.m., Research Applications in Digital Pathology
10 a.m., Diagnostic Applications in Digital Pathology
1 p.m., Teaching Applications in Digital Pathology
3 p.m., Research Applications in Digital Pathology
Friday, Sept. 7

8 a.m., Research Applications in Digital Pathology
1 p.m., Research Applications in Digital Pathology
3 p.m., Research Applications in Digital Pathology

Digital pathology, or ePathology, is a virtual platform for analyzing and sharing tissue specimens. The technology involves scanning and recreating a digital version of glass slides allowing for viewing, quantitative analysis, and real-time conferencing on virtual slides without the need for a microscope. The slides can be viewed and shared remotely, wherever an internet connection is available.

The sessions will feature information about digital pathology given by representatives from Aperio, a company specializing in digital slide scanning systems and related image software.  Complimentary slide scanning will be offered during the demonstrations for individuals interested in viewing specific prepared slides (limit two slides per person; please bring stained slides to the demonstration).

Sessions will last approximately one hour and will have specific themes such as research, diagnostic, and teaching applications in order to provide tailored information to varied audiences at UD and regional partner institutions. All sessions are open to UD researchers, regional partners and the public.

For more information and to register, visit this website.  For questions, contact Erin Brannick.


UD’s Schmidt studies genome of crocodile family in evolution research

June 14, 2012 under CANR News

University of Delaware scientist Carl Schmidt is working to identify genes in crocodiles, alligators and gharials as he searches for links between the creatures that could give clues as to how they evolved over the years in relation to one another.

Schmidt’s effort is part of a National Science Foundation-funded project being conducted by a team of researchers assembled by David Ray, an evolutionary biologist at Mississippi State University.

Schmidt, a professor in the Department of Animal and Food Sciences in UD’s College of Agriculture and Natural Resources (CANR), explained that his role in the study is to receive DNA sequences from researchers who collect samples from the three species.

Instead of trekking through the wetlands tracking down alligators, crocodiles and gharials — a crocodilian native to the Indian subcontinent — Schmidt is conducting all of his research on dry land in the safe confines of CANR’s Charles C. Allen Laboratory, with much of the DNA sequencing being done at the Delaware Biotechnology Institute (DBI). “They don’t let me chase the crocodiles,” he joked.

Along with Colin Kern, a UD doctoral student in the College of Engineering, Schmidt receives the DNA sequences and then uses different informatics approaches to identify the genes.

By identifying the genes that are commonly found in the DNA of the three creatures, Schmidt said that the researchers are able to predict where the genomic changes may have taken place.

This is particularly important when it comes to the gharial, which is an endangered species whose total world wide population numbers in the hundreds. “One of the things that I think is still a little unclear is the relationship of the gharials to the other crocodilians,” said Schmidt. “So one of the things we’re trying to tease out is the actual relationship between the gharials and the crocodiles.”

Because the gharial is so scarce, researchers have only been able to collect blood samples from the creature. In the case of the other two species, scientists have a variety of tissue samples, which allows for a broader array of DNA to be studied.

Despite the lack of tissue samples, the researchers are still confident that they will be able to discover the genomic changes, which in turn could lead to better conservation efforts to help the gharials avoid extinction.

Birds as Relatives

Schmidt’s work will eventually dovetail with a study being headed by Erich Jarvis, associate professor of neurobiology at Duke University Medical Center, and Mississippi State’s Ray that focuses on the genetic evolution of the closest living relative of the crocodilian family — birds.

Of the relationship between birds and crocodiles, Schmidt said, “It goes back to evolution in terms of crocodiles appearing to be the closest existing relatives of the birds, and the birds being modern dinosaurs, basically.”

Schmidt said that he is interested to see what genes are shared between birds and crocodiles, and which ones are unique to each creature — such as feathers for the birds — and he is hoping that they will be able to tie the results from the two studies together.

“A lot of it relates to how evolution has affected these two different lines of animals that share a fairly recent common ancestor,” Schmidt said, adding, “One of the things that I’m curious to find out is what the genome of that common ancestor looked like.”

Article by Adam Thomas

Photo by Danielle Quigley

This article can also be viewed on UDaily


ANFS Announces Fall Seminars

September 8, 2011 under CANR News, Events

The Department of Animal and Food Sciences has announced its Fall 2011 Seminar Series (ANRF 856) Schedule. Seminars are held on Mondays from 3:00 to 4:30 pm in 101 Allen Lab.  For more information contact the instructor: Dr. Serguei Golovan (046 Townsend, x7239, sgolovan@udel.edu).


Emergency response exercise set July 27

July 26, 2011 under CANR News

The University of Delaware will hold an emergency response exercise from 3-8 p.m., Wednesday, July 27, at the C.C. Allen Biotechnology Laboratory on the South Campus behind Townsend Hall, across from the Science and Technology Campus.

The exercise, which will help the University fine tune its emergency response protocols, is being conducted with the assistance of other state agencies and institutions. Participants will include the state of Delaware Emergency Management Agency, the Delaware departments of Agriculture, Public Health and Natural Resources and Environmental Control, as well as Christiana Care Health System at Christiana Hospital and Aetna Hose Hook and Ladder Co.

Because of the exercise, persons planning to visit the Outdoor Pool, the Ice Arenas or the UDairy Creamery the afternoon of July 27 should be aware that the access roads and parking lots behind the Townsend/Worrilow Hall complex will be blocked off for use by emergency vehicles and those participating in the exercise. Also closed during the exercise will be Sincock Lane, which runs behind the Nelson Athletic Complex from the Christina Parkway.


MSNBC news program features CANR chickens, ACRES hydrogen storage research

April 1, 2011 under CANR News

MSNBC came to campus asking questions about the future of energy. Thursday, March 31 the cable network aired what it learned.

UPDATE: See the aired segment online here: http://www.msnbc.msn.com/id/31510813/#42364876

Dylan Ratigan, host of The Dylan Ratigan Show, and a television crew taped a segment on the University of Delaware’s Affordable Composites from Renewable Sources (ACRES) program. Chemical engineering doctoral student Erman Senoz detailed in an interview how the research group uses chicken feathers to store hydrogen for use in cars, buses and other forms of transport.

The segment aired as part of the show’s “Steel on Wheelsfeature, which Ratigan labels as a road trip tackling the nation’s most important issues. He includes energy in that list.

The ACRES program, headed by Richard Wool, professor of chemical engineering, designs and develops bio-based materials for use in various renewable energy projects, from fuel cells to energy efficient housing.

While in Newark, the MSNBC crew taped at the College of Agriculture and Natural Resources‘ chicken houses, where Allen Laboratory manager Bob Alphin gave them a tour. They also viewed one of UD’s hydrogen buses, the product of work conducted by UD’s Center for Fuel Cell Research.

The original UDaily posting can be viewed online here.