Innovative Image De-Noising Method Helps Diagnose Schizophrenia
Biomedical Imaging
Student Stories
Graduate

Clinicians across the world now have access to an image de-noising “toolbox” that will allow them to improve the diagnosis and treatment of their patients with schizophrenia or bipolar disorder. This pre-processing algorithm enables scientists to compare, with greater specificity, brain scans of schizophrenic patients and healthy control subjects.

May. 17, 2011
Amy Mednick

Siddharth Khullar, a second year doctoral student at RIT’s Chester F. Carlson Center for Imaging Science, is pioneering new techniques that calibrate functional magnetic resonance imaging (fMRI) in more precise detail, allowing scientists to discern brain functionality of schizophrenic patients better than ever before.

“Neurodiseases don’t show up in a brain scan as readily as, for example, a brain tumor,” says Khullar, who studies with Center Director Stefi Baum. “If someone has a symptom of schizophrenia, or a similar disease such as bipolar disorder, they can take a cognitive test inside the fMRI scanner and, with this de-noising method, clinicians are able to compare and analyze the resulting images more accurately with the same scan of a healthy person.”

Even as Khullar works with Baum at RIT, he lives in sunny Albuquerque, New Mexico. He works as graduate research associate in the Medical Image Analysis Lab led by Vince Calhoun at the Mind Research Network for Neurodiagnostic Discovery. Khullar received a Master’s Degree in electrical engineering at RIT in 2009, and then started the Imaging Science PhD program and interned at the Mind Research Lab that summer. After a year of graduate classes at the Center, Khullar continued to work on his research at Mind Research Network and is currently funded by a federal grant (National Institutes of Health, PI Calhoun).

During his first year at the Mind Research Network, Khullar has already published a journal article and presented his findings at three major medical imaging conferences. And, he says, another journal article is in the works.

“I am thrilled about our association with the Mind Research Network,” says Baum, who is also an astrophysicist. “These types of partnerships emphasize the interdisciplinary and collaborative nature of our work at the Center. The expertise that Khullar is developing as an imaging science student will help medical professionals’ understanding and diagnoses of schizophrenia and other mental disorders.”

An fMRI scan captures the level of blood flow in the brain over time, similar to capturing a movie of the brain, yet ordinarily the image sequence produced is extremely difficult to quantify. Khullar’s method identifies and quantifies regions of activity in the fMRI brain images in a way that allows clinicians to differentiate characteristics of healthy and schizophrenic patients.

“We have shown, through our published work, that our algorithm is better in terms of preserving vital information about neural activation patterns within the brain,” Khullar says.

Next steps? In his most recent research, Khullar is working on a new pre-processing methodology that allows clinicians to compare the patient’s brain activity at rest and while the patient is conducting a simple activity such as pressing a button in response to a noise. Khullar’s new technique uses the observations of patient’s brain resting state activity to build an atlas representing the patient’s brain function that can be used to align the data obtained when the patient performs a task. This functional alignment enables improved fusion of data when studying a group of individuals who suffer from the same neurological ailment such as schizophrenia or even autism.  The aim is then to use that fused data to better understand what is happening in the brains of individuals with specific neurological conditions.  “My inherent goal is to make a broader impact on mankind,” Khullar says. 

Figure: This demonstrates a difference image from healthy controls (HC) and schizophrenia patients (SZ), showing regions in the temporal lobe that are relatively hyper active in healthy controls (red) and schizophrenia patients (blue). There is diminished activity in schizophrenia patients, probably a result of this neurodegenerative disease. These images were obtained using Khullar’s image denoising technique in addition to other segmentation algorithms.

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Imaging Science Grad Student Responds to Disaster Needs
Disaster Response
Remote Sensing
Student Stories
Graduate

A disaster, such as the devastating magnitude 9.0 earthquake and resulting tsunami that struck Japan this spring, can happen at any time and assessing damage proves difficult even when using aerial photography. Given the need to respond quickly when natural or man-made disasters occur, Chester F. Carlson Center for Imaging Science (CIS) graduate student Richard Labiak is developing a simple and quick tool that will supply emergency crews with rapid damage assessment within hours after a catastrophic event.

Jul. 19, 2011
Amy Mednick

Just days after Haiti experienced a magnitude 7.0 earthquake on January 12, 2010, scientists from CIS’s Digital Imaging and Remote Sensing Laboratory flew over the severely damaged Port-au-Prince region in a small plane equipped with a light detection and ranging (LiDAR) sensor.  These types of airborne laser scanners are able to collect high resolution, three-dimensional scans rapidly over large areas. The instrument, which sends out light pulses that hit a target and bounce back at up to 150,000 times a second, is often used for surveying and mapping of elevations. To assess damage without this technology, emergency crews rely on high-resolution photos taken from airplanes. This is a painstaking process that does not always accurately account for building heights and is limited by poor illumination or clouds and smoke.

When Labiak saw the LiDAR images, he realized he’d found an enormous, real-world opportunity to create an “interesting and relevant” master’s thesis using the DIRS’ dataset. 

Labiak envisions that while flying above a disaster scene, scientists would collect the LiDAR data and then his processing tool would use the data to produce a damage assessment map for disaster management workers.  “The ultimate goal is that an emergency will happen, we acquire airborne data, and then within a few hours, we are able to extract the relevant information, map it, and get it to people on the ground to show what is damaged and what is not,” says Labiak, who works with CIS Professor Jan van Aardt.

 

(click images to enlarge in new window)

This year Labiak discovered the less romantic side of scientific research as he spent hours analyzing data that combined high resolution Wildfire Airborne Sensor Program imagery collected simultaneously with LiDAR data. The grueling process of attempting to discern buildings from vegetation in one small section around Haiti’s National Palace, however, paid off. Labiak has come up with an important and useful tool that can provide a building map as well as an initial damage assessment. He presented his findings at the International Society for Optics and Photonics: Defense Security and Sensing Conference in April.

So far, the tool still requires a person to manipulate the data. “The tool is designed to be used in an operational setting, and hopefully will be helpful to disaster managers,” he says. “Eventually, the idea is to get it done pretty quickly and with as little human involvement as possible.”

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Doctoral Student Takes Her Archeological Imaging Research On the Road
Remote Sensing
Student Stories
Graduate

Oct. 7, 2011
Amy Mednick

Just back from a conference in Rio de Janeiro where she presented her research and received an international award, CIS doctoral student Kelly Canham is gearing up to pack her toothbrush, phrase book, and a spectroradiometer for a trip to Oaxaca, Mexico in December. There Canham will collaborate with William Middleton, associate professor of sociology and anthropology, to take ground-based spectral measurements to fill in some of the gaps left after analyzing the satellite data of the Nochixtlan Valley.

“The project in Nochixtlan will be for ground truthing various landscape taxa that Kelly has identified, and taking on-the-ground spectral measurements to better identify and interpret the satellite data,” Middleton says.

Canham found herself on her way to the Latin American GeoSpatial Forum in Brazil this August after winning Phase 2 of the Digital Globe 8-Band Research Challenge—one of five winners out of roughly 300 applicants worldwide. Canham proposed to apply an algorithm that she developed for examining hyperspectral data to Digital Globe’s multispectral WordView-2 satellite data. The Digital Globe WorldView-2 satellite data includes only eight spectral imaging bands compared to the 100s typical of hyperspectral data. The results Canham presented at the conference surpassed what was expected for a multispectral dataset.

 

Canham and David Messinger, Canham’s advisor and director of the Digital Imaging and Remote Sensing Laboratory, are developing image-processing tools to analyze hyperspectral satellite images so that Middleton can better understand the area of Oaxaca the Zapotec civilization once populated. Previously, archeologists had taken advantage of remote sensing imagery to identify individual sites by eye or to use a few spectral bands to find archaeological markers in the vegetation and terrain. The hyperspectral satellite data, obtained by the Hyperion sensor aboard NASA’s Earth Observing 1 satellite, includes many more spectral bands that form a ­­data cube and allow researchers to map the area in more detail.

Canham’s algorithm allows her to automatically analyze and identify the spectral signature of the materials located within each pixel in hyperspectral, and now multispectral, satellite images. The algorithm allows Canham to hypothesize, for example, that a given pixel might contain a small fraction of a material with a prominent spectral signature, which might be indicative of limestone rock. A larger fraction of that pixel might have a weak spectral signature, which could indicate an asphalt road. However, Canham and Middleton cannot verify this hypothesis until they actually survey the area by land to determine if the spectral signatures obtained through the analysis indicate the presence of limestone and asphalt.

In order to take the measurements necessary to create a spectral library of the area, Canham will use the FieldSpec Pro spectroradiometer. She won the use of this instrument from the Alexander Goetz Equipment Program last spring. A CIS microgrant will fund Canham’s travel expenses to Mexico. ( Seehttp://www.rit.edu/news/story.php?id=48248)

The eventual goal is to create a viable land-use map to add to Middleton’s research on the Zapotec civilization. “Overall, what we can do with hyperspectral data will never replace archaeologists, but we can help them look for "candidate" sites of interest,” Canham says. “Our goal is just to make their life a little easier and possibly, eventually, a bit cheaper than the old ground walking surveys.”

 

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CIS Student Enhances Digital Reconstruction of Tumors: Presents Findings at San Diego Medical Imaging Conference
Biomedical Imaging
Student Stories
Graduate

Biomedical researchers now have access to a more elegant method to digitally reconstruct microscopictissueslices, or histological sections, of tumor specimens into three-dimensional models thanks to the work of Shaohui Sun. 

Mar. 20, 2012
Amy Mednick

Sun—a Center for Imaging Science graduate student—presented his findings in February at the SPIE Medical Imaging Conference on Image Processing in San Diego.

CIS Professor Nathan Cahill discovered the problem in a conversation with Nzola de Magalhaes, a RIT Biomedical Engineering professor who studies tumor vascularization. Magalhaes wanted to find a way to stack successive histological sections of tumors in chicken embryos to eliminate the usual distortion and registration problems associated with digital reconstruction of these images.

Cahill, who is also a faculty member in the School of Mathematical Sciences faculty,  turned to his first-year graduate research assistant Sun to generate a mathematical algorithm to help solve the problem. “Shaohui spent a quarter learning about the limitations of prior techniques, developing the theory behind our new algorithm, implementing the new algorithm, and validating it on Nzola's data,” Cahill says.

Before he figured out the new algorithm, Sun says that Magalhaes used a much more laborious process of aligning the slices by hand. Previous techniques—extremely time consuming and difficult—produced only a course volumetric reconstruction of the tumors. Sun also needed to tackle the “aperture problem,” which is one of the main obstacles biomedical researchers face when attempting to digitally reconstruct three-dimensional specimens. When stacking 10s or 100s of these slices, the final result becomes twisted and distorted when examined next to the original specimen.

In the past, researchers have only looked at two successive images in the registration process. “I compared five to 10 images and then figured out the similarities between the slices. Once you have the matching features, you know what is in common and you can model a mathematical formula to solve the problem,” Sun says. Sun’s algorithm allowed him to compensate for rotational, scale, shear, and minute geometrical variations between the slices.

Cahill encouraged Sun to see this practical problem through to the end. “When Shaohui was able to establish that the new algorithm seemed to work well on Nzola's data (and performed better than more basic approaches), I knew that he had a good topic to submit to an international conference,” Cahill says.

Cahill and Sun wrote an abstract and submitted it to the SPIE Medical Imaging Conference over the 2011 summer. It was accepted for an oral presentation and, with Magalhaes, they wrote the full paper to submit to the conference proceedings. Sun, who is first author on the paper, presented his research at the RIT Graduate Research Symposium and at a seminar hosted by RIT's Center for Applied and Computational Mathematics. “By the time he gave the conference presentation, he had practiced enough so that he was able to do a great job,” Cahill says.

The work has useful applications, most directly, in research on tumor vascularization, but also in any application where histology is used such as cell growth and development, cancer research, and identification of pathologies, Cahill says.

Sun, 27, from Qingdao, China, says he appreciated the opportunity to attend the San Diego conference. “It was a great opportunity for me to gain experience from academic communities such as SPIE for my  professional development, and it will also enhance RIT's reputation in the field of medical imaging.”

Sun is currently working with CIS Professor Carl Salvaggio on a remote sensing study involving virtual three-dimensional building reconstruction of the RIT campus and downtown Rochester.

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RIT Doctoral Candidate Teaches ‘Computers to Understand Images’
Remote Sensing
Student Stories
Graduate

Abdul Haleem Syed wins best paper for automated image analysis

May. 23, 2012
Susan Gawlowicz

201205/abdul_syed.jpg

Image analysts can see the avalanche coming. A mountain of satellite imagery is growing faster than the rate at which they can turn data into useful pictures, such as a Google map.

Rochester Institute of Technology graduate student Abdul Haleem Syed ’08 (B.S., electrical engineering) is working to prevent imagery overload.

“Two hundred-eighty Earth observation satellites will be launched this decade compared to 135 launched in the previous decade,” says Syed, from Hyderabad, India. “That is a lot of images of Earth being collected but someone—usually an image analyst—has to manually work with these images to extract important information.”

Efficiently extracting useful bits of information from an image of a larger scene is at the heart of Syed’s doctoral research at RIT’s Chester F. Carlson Center for Imaging Science. He presented his novel research methods at the International Conference on Geographical Object-based Image Analysis May 7­–9 in Rio de Janeiro, Brazil, where he won best student paper for “Encoding of Topological Information in Multi-scale Remotely Sensed Data: Applications to Segmentation and Object-based Image Analysis.”

Syed co-authored the paper with his advisors, Eli Saber, professor of electrical engineering, and David Messinger, director of the Digital Imaging and Remote Sensing Laboratory in the Center for Imaging Science.

“My work involves teaching computers to understand images,” Syed says. “We want a computer to be able to look at an image and say, ‘That’s a road, that’s a building, and that’s a military compound.’ ”

Completely automated image analysis is Syed’s ultimate objective.

“Our more immediate goal is to reduce the burden of manual interpretation by developing tools that will help image analysts deal with the massive amount of satellite data that is being collected,” he says. “The paper I presented in Brazil helps solve a small piece of this big puzzle.”

Syed expects to graduate with his master’s and doctoral degrees from RIT’s Center for Imaging Science in May 2013. He looks forward to a career pursuing research in academia or industry.

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Original Source: University News

Astrophysics Ph.D. gives Trombley momentum
Astronomy and Space Science
Student Stories
Graduate

Apr. 26, 2013
Susan Gawlowicz

Christine Trombley keeps an ambitious to-do list. This May, she will check off her latest achievement—earning her Ph.D. from RIT’s astrophysical sciences and technology program.

“It is an amazing feeling to finally reach one of my primary goals in life,” Trombley says. “I have known I wanted a Ph.D. since I first started out as an undergraduate.”

Trombley, originally from Warren, Mich., studied the mass distribution of stars in clusters for her dissertation, “Investigation of the Intermediate and High End Initial Mass Function as Probed by near-Infrared Selected Stellar Clusters.” Her research at RIT led to an observing trip to Mauna Kea, Hawaii, and a three-month internship at the Goddard Space Flight Center in Greenbelt, Md., to gather data about groups of extremely large stars.

201304/christinetrombleykeck.jpg

Christine Trombley stands in front of the telescopes at the W. M. Keck Observatory on the summit of Mauna Kea, Hawaii. The RIT astrophysical sciences and technology graduate student will earn her Ph.D. this May.

“These stars are much more massive than the sun, even as much as 200 times more massive,” Trombley says. “The mass distribution of these stars can tell astronomers about massive star formation, a topic which remains a theoretical challenge.”

Trombley’s thesis adviser, Don Figer, director of RIT’s Center for Detectors, is an expert on massive stars.

“Christine’s research has been a tour de force representing work that she has done with me since 2007,” Figer says. “I expect her to go on and have a successful research career in the fields of massive stars and massive star clusters.”

The conferral of Trombley’s degree will bring closure to the inaugural class of astrophysical sciences and technology students that started the program in 2008, says Andrew Robinson, director of astrophysical sciences and technology.

“Christine was the first AST student to win an external fellowship—a NASA Graduate Student Research Fellowship—and when she graduates in May, she will also become the first woman to earn a Ph.D. in the AST program,” Robinson says.

Trombley is currently looking for a postdoctoral fellowship to continue her astrophysical research on massive stars and add to the collective understanding of the world.

“Astrophysics puts together the pieces of the puzzle of the universe,” she says. “If you are prepared to work hard, it’s possible to add your own contribution to understanding the nature of the universe.”

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Original Source: University News

Focus Area | Future of Research - National Technical Institute for the Deaf
Vision

The National Technical Institute for the Deaf (NTID) is a leader in the development of pedagogical theories and best practices for teaching deaf students. NTID researchers created C-Print®, real-time captioning, that is used in high school and college classrooms around the world. NTID faculty have numerous research projects underway that address how to integrate text, video, and graphics in the classroom when teaching students on various subjects, particularly the STEM disciplines.

Nov. 14, 2014
Kelly Sorensen

Visual Attention and Information Retention: Junior and senior faculty members from NTID and the Chester F. Carlson Center for Imaging Science are working together on research that examines deaf students’ gaze behavior associated with reading captions in videos of STEM lectures. Students may miss crucial information because they must divide their attention among the instructor, interpreter (or captioning screen), and the graphics. Researchers will investigate how the distance between captions and displays affects students’ ability to retain information.

Above, Kasmira Patel, a human-computer interaction major, watches a video about the periodic table in chemistry with professor Poorna Kushalnagar. The wall screen shows Patel’s gaze behavior.

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Original Source: RIT Research Magazine

Focus Area | Future of Research - College of Science
General

The College of Science continues to build on its collaborative, interdisciplinary, and multidisciplinary research and to develop new research clusters, laboratories, and centers. By applying the expertise of physicists, chemists, statisticians, mathematicians, computational scientists, and imaging scientists to human and environmental problems, researchers are developing novel solutions.

Nov. 14, 2014
Mark Gillespie

Breadth of Research

The college has well-established areas of research in imaging science, color science, detectors, astrophysical sciences, and the physical sciences. The college’s world-renowned Chester F. Carlson Center for Imaging Science generates millions in research funding annually and serves as the hub for its Ph.D. program in imaging science. Now, the college has its sights set on new innovations.

Analyzing Biomedical Imagery: Nathan Cahill, standing, along with imaging science doctoral student Kfir Ben Zikri, is developing algorithms for a longitudinal study of lung nodules in CT scans.

A new doctoral program in mathematical modeling is under development. This program will be interdisciplinary and provide graduates with a foundation in the development and application of mathematical models of real-world problems.

“Humanity’s challenges do not acknowledge the arbitrary categories of academic disciplines. The College of Science, therefore, isn’t afraid to combine the expertise of researchers across all of our disciplines,” said Sophia Maggelakis, dean of the College of Science.

The college is developing a portfolio of research clusters under the area of Bio+Sciences (biochemistry, biomathematics, biophysics, bioimaging, biotechnology, bioinformatics, and biostatistics). The college’s portfolio of research related to climate study and to STEM education continues to grow and has allowed partnerships with colleagues from other colleges and universities.

Undergraduate science and math students frequently work alongside faculty to conduct original research and regularly present at international and national conferences and publish, as co-authors, in peer-reviewed journals. The college is currently running three NSF-funded Research Experiences for Undergraduates (REU) programs.

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Original Source: RIT Research Magazine

A Look Back and the Road Ahead
Remote Sensing
Vision
Astronomy and Space Science

RIT is currently creating its blueprint for the next 10 years. Since the adoption of the last strategic plan in 2005, the university has transformed from a fine regional university to one of national prominence. The challenge ahead is how to become a world-class university without peer. 

Nov. 14, 2014
Ryne Raffaelle

Greater Emphasis on Scholarship and Research

Around the turn of the 21st century, RIT leadership instituted a new vision for research.

“We will be first in that class of universities that forms real, effective, and meaningful partnerships with industry and government,” said then RIT President Albert Simone when he announced his intentions. It was felt that the time had come for RIT to engage in an increased level of sponsored research and scholarly dissemination that would help the university emerge on the national stage. “First in Class” became the catch phrase.

This was partially in response to declining student demographics in the northeast and the need to expand the geographical base from which we were drawing students. RIT leadership also recognized that expanding the research portfolio would assist the university in what it had always done well—provide students with a hands-on experiential learning experience that would serve them well in their future careers. As student enrollment climbed, it was clear that additional resources would be required to provide meaningful research opportunities on campus to supplement the other hands-on experiences students received through their co-op placements and other opportunities, such as senior design projects.

In conjunction with the increasing level of sponsored research was an acknowledgement that competing at the national level for research funding would require an expansion of our terminal degree programs. Thus RIT added to its one pre-existing and very successful doctoral program in imaging science (1989). New Ph.D. programs were launched in microsystems engineering (2002), computing and information sciences (2005), color science (2007), astrophysical sciences and technology (2008), sustainability (2008), and engineering (2014).

Creation of Interdisciplinary Research Centers

Another trend at RIT was the transition from the model of an individual principal investigator (PI) working with an undergraduate or graduate student to one of interdisciplinary research centers. These centers incorporated multiple grants and PIs, many graduate and undergraduate students, and an increasing number of Ph.D. students and even some post-doctoral researchers. A new designation was established in 2009, titled RIT Research Centers of Excellence. These centers include the NanoPower Research Labs (NPRL), Digital Imaging and Remote Sensing Lab (DIRS), Multidisciplinary Vision Research Lab (MVRL), Laboratory for Multiwavelength Astrophysics (LAMA), Center for Detectors (CFD), Center for Computational Relativity and Gravitation (CCRG), Center for Advancing Science/ Mathematics Teaching, Learning and Evaluation (CASTLE), and Media, Arts, Games, Interaction and Creativity (MAGIC) Center. All of these initiatives resulted in dramatic growth in both the number of proposals and the number of new research awards received.

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Original Source: RIT Research Magazine

Student wins best paper award
Graduate
Remote Sensing

Imaging Science Ph.D. student recognized at IEEE Western New York Image Processing Workshop

Nov. 20, 2014

Jie Yang, a Ph.D. student in the Chester F. Carlson Center for Imaging Science, won the Best Remote Sensing Paper for “A Combined Approach for Ice Sheet Elevation Extraction from Lidar Point Clouds,” co-written with John Kerekes, professor in the Center for Imaging Science, at the IEEE Western New York Image Processing Workshop held at RIT on Nov. 7. Yang is a resident of Suizhou City, Hubei Province, China.

  

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Original Source: University News

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