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Ali
Can
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Woods
Hole Oceanographic Institution
Applied Ocean Physics
and Engineering Department
MS#7
Woods Hole, MA 02543 |
Work:
508-289-3740
acan@whoi.edu
http://www.cs.rpi.edu/~cana/ |
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Education
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Rensselaer
Polytechnic Institute,
Troy, NY
Ph.D. - Computer, Systems
Engineering |
8/2000 |
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Thesis
title: “Robust computer vision algorithms for registering images from curved
human retina.”
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M.S.
- Electrical Engineering
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5/1997
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Thesis
title: “Rapid automated tracing and feature extraction from live high-resolution
retinal fundus images using direct exploratory algorithms.”
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Gaziantep
University,
Gaziantep, Turkey
B.S. - Electrical Engineering |
6/1993
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Honors
and Awards
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·Microscopy
Society of America (MSA) Presidential Student Award, Microscopy & Microanalysis,
August 2002,Quebec
City, co-recepient.
·MSA
Presidential Student Award, Microscopy & Microanalysis, August 2000,
Philadelphia, PA.
·MSA
Advances in Instrumentation & Techniques 1st Prize, Student Award,
Microscopy & Microanalysis, August 2000, Philadelphia, PA. ·The
Allen B. DuMont Prize, Rensselaer Polytechnic Institute, May 2000, Troy,
NY. ·Best
Paper Award, the IEEE Conference on Computer Vision and Pattern Recognition
Conference, June 1999, Fort Collins, CO (Out of 500 submissions). |
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Experience
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Woods
Hole Oceanographic Institution (WHOI), Woods Hole, MA
Postdoctoral
Scholar |
9/2002-5/2004 |
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Lighting
Pattern and Attenuation Correction:
Corrected lighting pattern and attenuation in underwater imagery to increase
the performance of algorithms in applications such as image registration,
quantitative analysis, image enhancement, large-area mosaicing, and change
detection. Quantified the performance of different correction algorithms
by preparing a test-bed from the overlapping regions of registered images.
Collaborated with engineers at WHOI to incorporate these algorithms with
HB-LED lighting to revolutionize underwater lighting systems. Enhanced
underwater imagery by incorporating attenuation correction and registration
algorithms. These algorithms enable scattering free imaging even under
very adverse conditions.
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Change
Analysis of Ocean Floor:
Developing registration, segmentation, and classification algorithms to
examine a thirteen-year time series of photographs from the deep sea. These
algorithms automatically track animal movements to quantify the abundance,
size, and activity. These analyses of the longest deep-sea time-lapse sequence
will yield insights into deep-sea ecology.
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4D
Image Analysis and Motion Compensation:
Collaborate with researchers at Massachusetts General Hospital (MGH) to
design motion-compensated/adjusted treatment planning, and image-guided
radiotherapy. Developed algorithms to segment lungs, bones and tissues
in 4D CT data. By enabling rapid dose calculations, and accurate radiation
delivery, these algorithms can increase the dramatically low success rate
in radiation based cancer treatment.
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Generalized
Ocular Atlases for Ophthalmic Surgery:
Constructing 3D ocular atlases to achieve accurate treatment planning.
By accurately localizing the tumor relative to the ocular atlas, and relating
the exterior of the eye with the interior of the eye, this will lead to
real-time computer-assisted treatment methods such as online dosimetry
computation on the tumor, and safety shutoff mechanisms. Collaborated with
RPI and MGH radiation oncology department for this project.
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Rensselaer
Polytechnic Institute, Troy,
NY
Research Associate |
1/2002-9/2002 |
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Proton
Beam Radiation Eye Therapy:
Outlined the challenges and prospects related to image-guided proton beam
treatment, and ophthalmic treatment planning. Calibrated fundus microscopes,
and designed calibration targets for the x-ray system located at the proton-beam
facility at MGH. Analyzed different transformation models that represent
the imaging system distorted by multiple lenses. Supervised a graduate
student (Hari Iyer) to construct a 3D atlas of the eye using a simplified
projection model and ray tracing.
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Visiting
Scholar
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6/2001-9/2001
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Attenuation
Correction in Confocal Laser Microscopes:Developed
3D reconstruction, and 3D robust registration algorithms to extend the
lateral and axial dimensions of the confocal microscopy. Achieved attenuation
correction, and missing structure recovery by aligning and merging translated
and flipped confocal images. Supervised an RPI graduate student, Omar Al-Kofahi,
during this project.
Overcoming
the fundamental limitations of the confocal microscopes, this novel two-view
approach was awarded several awards by Microscopy Society of America.
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Research
Assistant, Ph.D.
Research
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8/1997-8/2000
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Robust
Computer Vision Algorithms:
Architected new algorithms to register retinal images, and create retinal
mosaics. Achieving accuracy and speed simultaneously, these new algorithms
lead to design of revolutionary change detection, and real-time computer
assisted treatment algorithms. Some of the contributions of my Ph.D. thesis
include;
·hierarchical
robust algorithms for simultaneous image registration and feature correspondence
estimation,
·new
linear, non-iterative method for jointly estimating the multi-image transformations, ·new
transformation model for registering images of curved human retina, ·gradual
graph construction algorithm for building up sufficient set of pairwise
image correspondences for joint estimation, ·quantitative
analysis techniques to measure the performance and accuracy of the algorithms. Awarded
the best paper award by the IEEE Computer Society, and the Allen B. DuMont
Prize by RPI, my Ph.D. research leaded to a 1.3 million dollar NSF grant,
and NIH R1-trust under the investigation of Prof. Badrinath Roysam. The
ongoing efforts at RPI are referred to as the retina project @ RPI which
has yielded several Ph.D. dissertations, and many publications and citations. |
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Research
Assistant, MS
Research
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1/1995-8/1997
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Exploratory
Feature Extraction Algorithms (MS Thesis):
Designed a template-based exploratory tracing algorithm for automatic,
rapid and accurate tracing of retinal vasculature. Achieved accuracy and
speed simultaneously by producing monotonically improving sequence of usable
partial results, and directly processing on the gray level data without
any pre-processing. Enabled the design of deadline-driven real-time computer
assisted treatment instrumentation.
Through
recent Ph.D. dissertations at RPI, this frequently cited algorithm has
been extended to build efficient and accurate 2D and 3D algorithms for
tracing neurons and vasculature. An FPGA hardware implementation of this
algorithm has recently been built at Boston University.
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Pharmaceutical
Imaging Applications:
Developed and implemented stage control, camera calibration and feature
extraction units of an automated Syrian Hamster Embryo cell transformation
assay classification system. Supervised several graduate and undergraduate
students to build parts of this real-time vision system.
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Inonu
University, Malatya, Turkey
Instructor |
8/2000-12/2001 |
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Taught
sophomore level probability class, and senior level digital communications,
and antenna theory classes. Participated in curriculum development activities
in the Electrical Engineering Department. Prepared a report on ABET substantial
equivalency requirements.
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Affiliations
and Committee Involvement
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NSF
ERC, Center
for Subsurface Sensing and Imaging Systems (CenSSIS).
Member,
IEEE Computer Society, Oceanic Engineering Society, and Microscopy Society
of America.
Reviewer
for IEEE
Journal of Oceanic Engineering, IEEE Transactions on Biomedical Engineering, and
IEEE Transactions on Information Technology in Biomedicine.
The
ORION Workshop participant in Primary Productivity and Ecology, and Engineering
and Technology groups, January 2004, San Juan, Puerto Rico.
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Research
Cruises
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Oxygenated
and Anoxic waters of Black Sea, Sinop, Turkey, Chief Scientist R.
Ballard, RV Knorr, “Deep underwater archaeology,” three weeks in August
2003. (This cruise appeared as a featured article in May 2004 issue of
National Geographic Magazine)
Marine
Conservation District Hind Bank and the South Drop, St. Thomas and St.
John in the US Virgin Islands, Chief Scientist H. Singh, RV Chapman,
“Deepwater coral reefs research,” one week in June 2003.
Stellwagen
Bank Marine Sanctuary Region, Boston, Massachusetts, Chief Scientist
H. Singh, RV Oceanus, “Geologic and Benthic-Habitat Studies of the Sea
Floor,” one week in March 2003.
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Journal
Publications
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Al-Kofahi,
K., A. Can, S. Lasek, D. H. Szarowski, N. Dowell, W. Shain, J. N.
Turner, B. Roysam “Median Based Robust Algorithms for Tracing Neurons from
Noisy Confocal Microscope Images,” IEEE Transactions on Information
Technology in Biomedicine, vol. 7, no. 4, pp. 302-317, December, 2003.
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Can,
A.,
O. Al-Kofahi, S. Lasek, D. H. Szarowski, J. N. Turner, B. Roysam, “Attenuation
Correction in Confocal Laser Microscopes: A Novel Two-view Approach,” Journal
of Microscopy, vol. 211, pp. 67-79, July 2003.
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Al-Kofahi,
O., A. Can, S. Lasek, D. H. Szarowski, J. N. Turner, B. Roysam,
“Registration of 3-D Neuron Images Acquired by Confocal Scanning Laser
Microscopes,” Journal of Microscopy, vol. 211, pp. 8-18, July 2003.
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Can,
A.,
C. V. Stewart, B. Roysam, H. L. Tanenbaum, “A Feature-Based Technique for
Joint, Linear Estimation of High-Order Image-to-Mosaic Transformations:
Mosaicing the Curved Human Retina,” IEEE Transactions on Pattern Analysis
and Machine Intelligence, vol. 24, no. 3, pp. 412-419, March 2002.
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Can,
A.,
C. V. Stewart, B. Roysam, H. L. Tanenbaum, “A Feature-Based, Robust, Hierarchical
Algorithm for Registering Pairs of Images of the Curved Human Retina,”
IEEE
Transactions on Pattern Analysis and Machine Intelligence, vol. 24,
no. 3, pp. 347-364, March 2002.
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Turner,
J. N., W. Shain, D. H. Szarowski, S. Lasek, N. Dowell, B. Sipple, A.
Can, K. Al-Kofahi, B. Roysam, “Three-Dimensional Light Microscopy:
Observation of Thick Objects,” The Journal of Histotechnology, vol.
23, no. 3, pp. 205-217, September 2000.
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Can,
A.,
H. Shen, J. N. Turner, H. L. Tanenbaum, B. Roysam, “Rapid Automated Tracing
and Feature Extraction from Live High-Resolution Retinal Fundus Images
Using Direct Exploratory Algorithms,” IEEE Transactions on Information
Technology in Biomedicine, vol. 3, no. 2, pp. 125-138, June 1999.
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Turner,
J. N., W. Shain, D. H. Szarowski, S. Lasek, B. Sipple, C. Pace, K. Al-Kofahi,
A.
Can, B. Roysam, “Confocal Light Microscopy of Brain Cells and Tissue:
Image Analysis & Quantitation,” Acta Histochemica et Cytochemica,
vol.
32, No. 1, pp. 5-11, 1999.
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Becker,
D. E., A. Can, H. L. Tanenbaum, J. N. Turner, B. Roysam, “Image
Processing Algorithms for Retinal Montage Synthesis, Mapping, and Real-Time
Location Determination,” IEEE Transactions on Biomedical Engineering,
vol.
45, no. 1, pp. 105-118, January 1998.
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Book
Chapters
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Fritzsche,
K., A. Can, H. Shen, C. Tsai, J. N. Turner, H. L. Tanenbaum, C.
V. Stewart, B. Roysam “Automated Model-Based Segmentation, Tracing, and
Analysis of Retinal Vasculature from Digital Fundus Images,” Angiography
and Plaque Imaging, Advanced Segmentation Techniques, CRC Press, pp.
225-297, 2003.
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Becker,
D. E., A. Can, H. L. Tanenbaum, J. N. Turner, B. Roysam, “Image
Processing Algorithms for Retinal Montage Synthesis, Mapping, and Real-Time
Location Determination,” IMIA Yearbook of Medical Informatics, International
Medical Informatics Association, Schattauer Press, Germany, (Bemmel
et al., eds), pp. 433-446, 1999.
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Conference
Publications
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Paganetti,
H., E. Rietzel, A. Can, H. Singh, G. T. Y. Chen, “Real
Four-Dimensional Monte Carlo Dose Calculation for Double-Dynamic Systems
(Time-Dependent Delivery Under Organ Motion),” Medical Physics,
vol. 30, page 1451 (Abstract), San Diego, CA, August 2003.
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Paganetti,
H., E. Rietzel, A. Can, H. Singh, G. T.Y. Chen, “Simulation of four-dimensional
effects in radiation therapy: The dose in intensity modulated beam delivery
under organ motion,” International Journal of Radiation Oncology, Biology,
and Physics, Salt Lake City, Utah, October 2003.
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Al-Kofahi,
O., A. Can, S. Lasek, D. H. Szarowski, J. N. Turner, B. Roysam,
"Multi-View Three-Dimensional Image Montaging & Signal Attenuation
Correction for Maximizing the Imaging Depth and Lateral Extend of Confocal
Microscopes," Proceedings Microscopy and Microanalysis, Microscopy Society
of America 60th Annual Meeting, Quebec City, Canada, pp. 1042-1044,
August 2002. (MSA Presidential Student
Award, co-recipient)
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Can,
A.,
S. Lasek, D. H. Szarowski, J. N. Turner, B. Roysam, “A Robust Two-View
Method for Increasing the Imaging Depth and Correcting for Signal Attenuation
in Confocal Microscopes,” Proceedings Microscopy and Microanalysis,
Microscopy Society of America 58th Annual Meeting, Philadelphia, Pennsylvania,
pp. 818-819, August 2000. (MSA
Presidential Student Award)
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Can,
A.,
C. V. Stewart, B. Roysam, H. L. Tanenbaum, “A Feature-Based Technique for
Joint, Linear Estimation of High-Order Image-to-Mosaic Transformations:
Application to Mosaicing the Curved Human Retina,” Proceedings IEEE
Computer Society Conference on Computer Vision and Pattern Recognition,
Hilton
Head Island, South Carolina, pp. 585-591, June 2000.
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Can,
A.,
C. V. Stewart, B. Roysam, “Robust Hierarchical Algorithm for Constructing
a Mosaic from Images of the Curved Human Retina,” Proceedings IEEE Computer
Society Conference on Computer Vision and Pattern Recognition, Fort
Collins, Colorado, pp. 286-292, June 1999. (Best Paper Award)
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Roysam,
B., A. Can, H. Shen, J. N. Turner, “From 3-D Light Microscopic Images
to Quantitative Insight,” Proceedings Microscopy and Microanalysis,
Microscopy Society of America 57th Annual Meeting, Portland, Oregon,
pp. 524-525, August 1999.
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Turner,
J. N., W. Shain, D. H. Szarowski, S. Lasek, L. Kam, A. Can, K. Al-Kofahi,
B. Roysam, “Three-Dimensional Light Microscopy: Imaging & Corrections
for Quantitative Analysis,” Proceedings Microscopy and Microanalysis,
Microscopy Society of America 57th Annual Meeting, Portland, Oregon,
pp. 522-523, August 1999.
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Can,
A.,
H. Shen, K. Al-Kofahi, J. N. Turner, H. L. Tanenbaum, B. Roysam, “Rapid,
Automated, and Robust Tracing of Vasculature, and Quantification of Visual
Features from Angiographic Images,” Proceedings Microscopy and Microanalysis,
Microscopy Society of America 55th Annual Meeting, Cleveland, Ohio,
pp. 325-326, August 1997.
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Manuscripts
Submitted and in Preparation
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Can,
A.,
H. Singh, “Methods for Correcting Lighting Pattern and Attenuation in Underwater
Imagery,” submitted for review to IEEE Journal of Oceanic Engineering,
May 2004.
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Singh,
H., A. Can, E. Ryan, S. Lerner, N. McPhee, O. Pizarro, C. Roman,
“The Seabed AUV: A new platform for High Resolution Imaging,” submitted
for review to EOS, Transactions, American Geophysical Union, May
2004.
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Can,
A.,
H. Singh, G. Yang, B. Roysam, C. V. Stewart,
“Optimal Blending Algorithms for Large-area Color Mosaics,” in preparation
for IEEE Transactions on Pattern Analysis and Machine Intelligence.
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Beaulieu,
S.E., A. Can, H. Singh, K.L. Jr. Smith, “Analyzing Time-lapse Photographs
of the Sea Floor for Changes in Benthic Community Activity,” in preparation
for Limnology and Oceanography: Method.
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Can,
A.,
H. Singh, G. Yang, G. Lin, B. Roysam,
C. V. Stewart, G. Chen, J. M. Collier, “Construction of 3-D Generalized
Ocular Atlases,” in preparation for Journal of the Optical Society of
America A – Optics, Image Science, and Vision.
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A
Few Pictures
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