Primary home page: http://www.ecse.rpi.edu/~roysam

Office: Rm. 7010, Jonsson Engineering Center

Rensselaer Polytechnic Institute, 110, 8th Street, Troy, New York 12180-3590

Office: (518) 276-8067, Lab: (518) 276-8207/8193,

Assistant (Laraine): (518) 276-8525, Fax: (518) 276-8715

BACKGROUND

I received my bachelors degree in electronics from the Indian Institute of Technology, Madras in 1984. I then went to Washington University, St. Louis, Missouri where I received my Masters in electrical engineering (1987), and a doctorate in electrical engineering (1989). I have been a faculty member at Rensselaer since then.

RECENT TEACHING

Intro to Subsurface Sensing and Imaging Systems

Cell and Tissue Image Analysis

STUDENT AWARDS AND ACHIEVEMENTS

I am proud of my students – here are some of their achievements.

 

1.       Andrew Cohen and Phil Getto were co-authors on 1991 IEEE IAS Conference Prize Paper Award, and subsequent invited publication [8].

2.       Anoop Bhattacharjya was selected to attend the prestigious 1993 Summer School on Connectionist Models. This school is attended by approximately 50 doctoral students selected by a worldwide competition.

3.       Hakan Ancin won a 1993 Presidential Student Award from the Microscopy Society of America for his paper, “Automated 3-D Cell Population Analysis in Thick Tissue Sections from Laser-Scanning Confocal Microscopy Data.” This honor is bestowed upon approximately 6-8 students based on a worldwide competition.

4.       Robert Mackin won the 1994 Presidential Student Award from the Microscopy Society of America.

5.       Ali Can was first author on a paper that won the Best Paper Award at the 1999 IEEE Conference on Computer Vision and Pattern Recognition, Fort Collins, CO.

6.       Ali Can won the Presidential Student Award at the 2000 Annual Meeting of the Microscopy Society of America, Philadelphia for his work on increasing the depth of imaging in laser-scanning confocal microscopy.

7.       Hong Shen won the Charles M. Close ‘62 Doctoral Prize, Spring 2000.

8.       Ali Can won the Allen B. Dumont Prize for his doctoral work, Spring 2000.

9.       Khalid Al-Kofahi won the Allen B. Dumont Prize for his doctoral work, Spring 2001.

10.   Omar Al-Kofahi worn the MSA Presidential Student Award, August 2002.

11.   Saurabh Roy won a Student Travel Award from the International Society for Analytical Cytology in January 2002.

12.   Saurabh Roy received a fellowship to attend the 2nd International Summer School on BIOCOMPLEXITY FROM SYSTEM to GENE sponsored by the NSF and co-sponsored by the IEEE EMB Society, July 2002.

13.   Leah Fisher won an undergraduate research award from Intel Corp., 2002.

14.   Amri Muhammad Abdul-Karim won the MSA Presidential Student Award, 2003.

15.   Amri Muhammad Abdul-Karim won the Nolte Prize from the ECSE Department, Spring 2003.

16.   James Alex Tyrrell along with Vijay Mahadevan won the presidential student award from the Microscopy Society of America, 2004.

17.   James Alex Tyrrell won the Rensselaer Founders Award for Excellence, Oct 2004.

18.   Hari Iyer won the presidential student award from the Microscopy Society of America, 2005.

19.   Harihar Narasimha Iyer won the Rensselaer Polytechnic Institute Founders Award for Excellence, 2005.

20.   Ying Chen won the Presidential Student Award from the Microscopy Society of America, 2006.

21.   Yousef Al-Kofahi won the Presidential Student Award from the Microscopy Society of America, 2007.

1.       Arun Narayanaswamy won the the Presidential Student Award from the Microscopy Society of America, 2008.

RESEARCH INTERESTS

My lab develops multi-dimensional image analysis algorithms in service of applications in biology and medicine (talk). We collaborate with a long and growing list of colleagues in diverse disciplines. You can see some of that as you browse our list of papers (below).

The world of biology is on the move – biological investigations are shifting (i) from qualitative and observational towards quantitative; (ii) from reductionist approaches towards the study of integrated systems consisting of multiple interacting components; (iii) from sequential experimentation towards high-throughput and high-content studies; and (iv) from static observations of fixed tissue towards dynamic observations of living tissue.

Aside from increased demand for quantitation, there is a fundamental shift in the types of quantitative measurements and inferences that are sought from images. For example, integrative studies of complex systems (e.g., brain tissue) require measurements of structural and functional relationships among the components of the system, in addition to traditional morphometry of the components. The emergence of imaging-driven systems biology is another source of demand for image analysis technology. Increasingly, biochemical and biophysical models are being mapped to spatial compartments derived from actual microscopy data to achieve unprecedented realism in computational biology. Imaging is essential for studying cell behaviors that depend on morphology, connectivity, and spatial relationships with neighboring structures.

Biological Image Analysis: In the biology area, much of my current activities revolve around characterization of complex systems such as neurovascular stem-cell microenvironments, cortical tissue surrounding neuroprosthetic devices (see figure below), analyzing the dynamics of stem-cell differentiation in vitro, optimization of engineered tissue constructs, and mapping embryonic development in vivo. A major recent focus of my laboratory has been on stem cells and functional tissue engineering. This is a collaborative project with many partners. A summary of these efforts can be found in this talk.

 

We work on images that are 3-D, multi-temporal, multi/hyper-spectral (indicating multiple chemical species), and from multiple modalities. They are challenging to process, due to high variability and size. They require combinations of techniques, including statistical modeling, reconstruction (talk), enhancement, segmentation, registration, robust estimation, pattern analysis, and web/parallel programming. These tasks are computationally demanding; therefore, high-performance computing is an integral part of our work.

The FARSIGHT project in my laboratory is developing multi-dimensional image analysis tools that can handle the burgeoning complexity and volume of modern microscopy data; and the image-based measurement needs of modern biology. (talk)

Modern optical microscopy has emerged as a tool of choice for conducting diverse biological investigations at the sub-cellular, cellular, and tissue levels. The widespread availability of confocal and multi-photon microscopes and high-NA objectives, have made high-resolution (axial and lateral) three-dimensional (3-D) imaging of multiple structures and functional markers routine. Burgeoning libraries of organic and inorganic fluors (such as conjugated quantum dots) enable simultaneous labeling of multiple structural and functional markers. Fluorescent protein tagging enables imaging of processes in living systems. Time-lapse imaging of living tissue is enabled by controlled-environment chambers, and minimally-damaging imaging modalities.

By combining techniques, processes such as morphological and chemical dynamics, molecular transport, chemical dynamics, gene circuits, and signaling can be recorded. Furthermore, these processes can be recorded in the spatial context of intact tissue, unlike techniques like arrays and flow cytometry that disrupt spatial information. The availability of spectral- and time-resolved photon detection systems is enabling fluorescence spectral lifetime studies. The availability of “fusion microscopes” that incorporate multiple imaging modalities on the same platform allows measurement of multiple types of spatial, biochemical, and physical measurements. Finally, a set of supporting technologies ranging from image pre-processing software to high-throughput specimen preparation instruments have further magnified the capabilities of optical microscopy.

SOFTWARE TOOLS

Two examples of software tools developed in our laboratory are Quantitative 3D-catFISH (Compartmental and Temporal Analysis of Fluorescence In-Situ Hybridization Signals) and RPI-Trace3D. Quantitative cat-FISH is an innovative software program that can quantify the spatio-temporal patterns of immediate early gene transcription activity from multi-dimensional images of rat hippocampi after the animals have run through specially designed cognitive tasks such as mazes (talk). RPI-Trace3D can rapidly trace neurons, provide detailed morphometry, and analyze changes over time. It has been commercialized by MBF Bioscience. It is being used at the Wadsworth Center to quantify the patterns of growth of neurons on nano-engineered surfaces (talk). It is being used at Harvard Medical School to quantify changes in tumor microvasculature. It is being used at Wadsworth to quantify vascular changes caused by the insertion of neural implants. Our current focus is on developing a new generation of associative image analysis tools named FARSIGHT. Here is what it looks like on our screen.

Biomedical Image Analysis: The Retina project at Rensselaer is developing core image analysis technologies that can enable a new generation of ophthalmic instruments that are “spatially aware.” This new generation of instruments will have a built-in robust computer vision system that detects the key structures of the retina, tracks them over time, and maintains a dynamically updated map of the entire retina. Using such a map provides important advantages. For example, spatial referencing relative to a pre-computed map avoids the drift problem that is endemic to traditional tracking algorithms. This core computer vision-based system can be employed in diverse retinal applications as a building block (talk).

This is a multi-faceted project, and involves a large number of collaborators, and algorithms for vascular and non-vascular feature extraction, registration, real-time tracking, parallel/multi-threaded computation, change detection, change classification, and the construction of integrated hardware/software systems. A particular emphasis of this project has been the development of opportunistic and exploratory computer vision approaches that are designed for real-time use. For instance, our algorithms perform just-sufficient and highly-prioritized feature extraction to perform real-time spatial referencing. To make such systems work in real time in a predictable manner, we have had to develop elaborate methods to migrate large and sophisticated computer vision algorithms to the linux kernel space.

A recent emphasis area for the Retina project has been the analysis of changes over time (longitudinal changes) occurring in human retinas. We are interested in structural as well as functional changes. A talk summarizing this aspect is available. (talk)

JOURNAL PUBLICATIONS

Note: Names of my students or post-doctoral associates are highlighted. The pdf links below are a personal-use courtesy to my students and colleagues. The copyrights for these items belong with the respective publishers.

  1. Miller, M.I., B. Roysam, J.E. Saffitz, K.B. Larson, D. Fuhrmann, and L.J. Thomas, Jr., "A New Method for the Analysis of Electron Microscopic Autoradiographs," Biotechniques, vol.  5, No. 4, pp. 322-328, 1987. (pdf)
  2. Fuhrmann, D. R., Brown, M. A. , Miller, M. I., Roysam, B., Saffitz, J. E., and Thomas Jr., L. J., "Data Acquisition System for Maximum-Likelihood Analysis of Electron Microscopic Autoradiographs," Journal of Microscopy Research and Technique, vol. 7, no. 3, pp. 199-204, November 1987. (pdf)
  3. Miller, M. I., and B. Roysam, "Bayesian Image Reconstruction for Emission Tomography Incorporating Good's Roughness Prior on Massively Parallel Processors," Proceedings of the National Academy of Sciences, Vol. 88, No. 8, pp. 3223-3227, April 1991. (pdf)
  4. Miller, M. I., Roysam, B., Smith, K. R., O'Sullivan, J. A., "Representing and Computing Regular Languages on Massively Parallel Networks," IEEE Transactions on Neural Networks, Vol. 2, No. 1, pp. 56-72, January, 1991. (pdf)
  5. Roysam, B. Maffitt, D. R., and Miller, M. I., Saffitz, J. E., and Thomas Jr., L. J. , "A Personal Computer Based Implementation of the Maximum-Likelihood Method of Analysis of Electron Microscope Autoradiographs," Journal of Microscopy Research and Technique, vol. 20, No. 1, pp. 73-86, January 1992. (pdf)
  6. Roysam, B., and Bhattacharjya, A. K., "Hierarchically-Structured Unit Simplex Transformations for Parallel Distributed Optimization Problems," IEEE Transactions on Neural Networks, Vol.3, No. 1, pp. 108-114, January 1992. (pdf)
  7. Bhattacharjya, A. K., Becker, D., and Roysam, B., "A Genetic Optimization Algorithm for Intelligent Imaging with Quantum-Limited Data," Signal Processing, Elsevier Science Publishers, Vol. 28, No. 3, pp. 335-348, 1992.(pdf)
  8. Roysam, B., Miller, M. I., “Combining Stochastic and Syntactic Processing with Analog Computation Methods,” Digital Signal Processing: A Review Journal, John Hershey (Ed.), Vol. 2, No. 2, pp. 48-64, April 1992 (invited paper). (pdf)
  9. Roysam, B., Bhattacharjya, A. K., Srinivas, C., and Turner, J. N., "Unsupervised Noise Removal Algorithms For 3-D Confocal Fluorescence Microscopy," Micron and Microscopica Acta, Vol. 23, No. 4, pp. 447-461, December 1992. (pdf)
  10. Roysam, B., Cohen, A., Getto, P. H., and Boyce, P. R., "A Numerical Approach to the Computation of Light Propagation through Turbid Media: Application to the Evaluation of Lighted Exit Signs," IEEE Transactions on Industry Applications, Vol. 29, No. 3, pp. 661-669, May./June 1993 (invited paper). (pdf)
  11. Willis, B., Turner, J. N., Collins, D. N., Roysam, B., and Holmes, T. J., “Developments in Three Dimensional Stereo Brightfield Microscopy,” Journal of Microscopy Research and Technique, Vol. 24, No. 5, pp. 437-451, April 1993. (pdf)
  12. Willis, B., Roysam, B., Turner, J. N., and Holmes, T. J., “Iterative, Constrained 3-D Image Reconstruction of Transmitted Light bright-field Micrographs Based on Maximum-Likelihood Reconstruction,” Journal of Microscopy, Vol. 169, Pt. 3, pp. 347-361, March 1993. (pdf)
  13. Roysam, B., Review of: Computational Vision by Harry Wechsler, SIAM Review, Vol. 35, No. 1, pp. 165-166, March 1993.
  14. Mackin, R. W., Roysam, B., Holmes T. J., and J. N. Turner, "Automated Image Analysis of Thick Cytological Preparations Using 3-D Microscopy And 3-D Image Analysis: Application To Pap Smears," Analytical and Quantitative Cytology and Histology, vol. 15, pp. 405-417, December 1993. (pdf)
  15. Bhattacharjya, A. K., and Roysam, B., "Joint Solution of Low, Intermediate and High-Level Vision Tasks by Evolutionary Optimization: Application to Computer Vision at Low SNR,” IEEE Transactions on Neural Networks, vol. 5, no. 1, pp. 83-95, January 1994. (pdf)
  16. Roysam, B., Ancin, H., Bhattacharjya, A., K., Chisti, M. A., Seegal, R., and Turner, J. N., "Algorithms for Automated Cell Population Analysis in Thick Specimens from 3-D Confocal Fluorescence Microscopy Data," Journal of Microscopy, Vol. 173, Pt. 2, February 1994. (pdf)
  17. Cohen, A. R., Roysam, B., and Turner, J. N., "Automated Tracing and Volume Measurements of Neurons from 3-D Confocal Fluorescence Microscopy Data," Journal of Microscopy, Vol. 173, Pt. 2, February 1994. (pdf)
  18. Turner, J. N., Szarowski, D. H., Turner, T. J., Ancin, H., Lin, W., Roysam, B., and Holmes, T. J., "Three-Dimensional Imaging and Image Analysis of Hippocampal Neurons: Confocal and Digitally Enhanced Wide Field Microscopy," Journal of Microscopy Research and Technique, Vol. 29, No. 4, November 1994. (pdf)
  19. Ancin H., Roysam B., Dufresne T. E., Chestnut M. E., Ridder G. M., Szarowski D. H., and Turner J. N., “Advances in Automated 3D Image Analysis of Cell Populations Imaged by Confocal Microscopy,” Cytometry, Vol. 25, No. 3, pp. 221-234, November 1996. (pdf)
  20. Becker D. E., Ancin H., Szarowski D. H., Turner J. N., and Roysam B., “Automated 3-D Montage Synthesis from Laser-Scanning Confocal Images: Application to Quantitative Tissue-Level Cytological Analysis,” Cytometry, Vol. 25, No. 3, pp. 235-245, November 1996. (pdf)
  21. Turner, J. N.,  Ancin, H., Becker, D., Szarowski, D. H., Holmes, M. O’Connor, N., Wang, M., Holmes, T. J., and Roysam, B., “Automated Image Analysis Technologies for Biological 3-D Light Microscopy,” Vol. 8, pp.240-254, International Journal of Imaging Systems and Technology, Special Issue on Microscopy, John Wiley & Sons, 1997. (pdf)
  22. Becker, D. E., Ali Can, Tanenbaum, H. L., and Turner, J. N., Roysam, B., “Image Processing Algorithms for Retinal Montage Synthesis, Mapping, and Real-Time Location Determination,” IEEE Transactions on Biomedical Engineering, vol. 45, No. 1., January 1998. (pdf)
  23. Robert W. Mackin, Jr., Louise M. Newton, James N. Turner, Badrinath Roysam, “Advances in High-Speed Three-Dimensional Imaging and Automated Segmentation Algorithms for Thick and Overlapped Clusters in Cytologic Preparations: Application to Cervical Smears,” Vol. 20, No. 2, pp. 105-121, Analytical and Quantitative Cytology and Histology, 1998. (pdf)
  24. Robert W. Mackin, Jr., Louise M. Newton, James N. Turner, Timothy J. Holmes, Badrinath Roysam, “The Quantitative Impact of Computational Deblurring and 3-D Feature Computation on the Accuracy of Nuclear Classification in Cervical Smear Images,”  Analytical and Quantitative Cytology and Histology, Vol. 20, No. 2, pp. 72-91, 1998. (pdf)
  25. Can, A., H. Shen, J. N. Turner, H. L. Tanenbaum, and 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. (pdf)
  26. Becker, D. E., Ali Can, Tanenbaum, H. L., and Turner, J. N., Roysam, B., “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. (pdf)(editorial)
  27. Turner, J.N., Shain, W., Szarowski, D.H., Lasek, S., Sipple, B., Pace, C., Al-Kofahi, K., Can, A., and Roysam, B.  Confocal Light Microscopy of Brain Cells and Tissue: Image Analysis & Quantitation.  Acta Histochemica et Cytochemica, vol. 32, No. 1, pp. 5-11, 1999. (pdf)
  28. Shain, W., Turner, J. N., Szarowski, D. H., Davis-Cox, M., Ancin, H., and Roysam, B., “Application and Quantitative Validation of Computer-Automated 3-D Counting of Cell Nuclei in Brain Tissue,” Microscopy and Microanalysis, vol. 5, no. 2, pp. 106-119, 1999. (pdf)
  29. Ostrander, L., and Roysam, B., “Tailoring an Introductory Course in Biomedical Imaging,” The International Journal of Engineering Education, Tempus Publications, vol. 15, No. 4, 1999. (pdf)
  30. Turner, J. N., Shain, W., Szarowski, D. H., Lasek, S., Dowell, N., Sipple, B., Can, A., Kofahi, K. A., and Roysam, B., “Three-Dimensional Light Microscopy: Observation of Thick Objects,” The Journal of Histotechnology, vol. 23, No. 3, September 2000. (pdf)
  31. Hong Shen, Badrinath Roysam, Charles V. Stewart, James N. Turner, and Howard L. Tanenbaum, “Optimal Scheduling of Tracing Computations for Real-time Vascular Landmark Extraction from Retinal Fundus Images,” IEEE Transactions on Information Technology in Biomedicine, vol.5, No. 1, March 2001. (pdf)
  32. Can, A., Stewart, C. V., Roysam, B., and Tanenbaum, H. L., “A Feature-Based Robust Hierarchical Algorithm for Registration Pairs of Images of the Curved Human Retina,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 24, no. 3, March 2002. (pdf)
  33. Can, A., Stewart, C. V., Roysam, B., and Tanenbaum, H. L., “A Feature-Based Algorithm 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, March 2002. (pdf)
  34. Khalid Al-Kofahi, Sharie Lasek, Donald Szarowski, Christopher Pace, George Nagy, James N. Turner, Badrinath Roysam, “Rapid Automated Three-dimensional Tracing of Neurons from Confocal Image Stacks,” IEEE Transactions on Information Technology in Biomedicine, vol. 6, No. 2, June 2002. (pdf)
  35. Shen, H., Stewart, C. V., Roysam, B., Lin, G., and Tanenbaum, H. L., “Frame-Rate Spatial Referencing Based on Invariant Indexing and Alignment with Application to Laser Retinal Surgery,” vol. 25, No. 3, pp. 379-384, IEEE Transactions on Pattern Analysis and Machine Intelligence, March 2003. (pdf)
  36. Wenyun He, Thomas A. Hamilton, Andrew R. Cohen, Timothy J. Holmes, James N. Turner, and Badrinath Roysam, “Automated Three-Dimensional Tracing of HRP Stained Neurons From A Stack Of Brightfield Optical Slices,” Microscopy and Microanalysis, vol. 9, 296-310, 2003. (pdf)
  37. Al-Kofahi, O., Can, A., Lasek, S., Szarowski, D. H., Turner, J. N., and Roysam, B., “Hierarchical Algorithms for Affine 3-D Registration of Neuronal Images Acquired by Confocal Laser Scanning Microscopy,” Journal of Microscopy, vol. 211, part 1, pp 8-18, July 2003. (pdf)
  38. Can, A., Al-Kofahi, O., Lasek, S., Szarowski, D. H., Turner, J. N., and Roysam, B., “Attenuation Correction in Confocal Laser Microscopes: A Novel Two-View Approach,” Journal of Microscopy, vol. 211, part 1, pp 67-79, July 2003. (pdf)
  39. Muhammad-Amri Abdul-Karim, Khalid Al-Kofahi, Edward B. Brown, Rakesh K. Jain, Badrinath Roysam, “Automated Tracing And Change Analysis Of Tumor Vasculature From In Vivo Multiphoton Confocal Image Time Series,” Microvascular Research, Volume 66, Issue 2 , Pages 113-125, September 2003. (pdf)
  40. Gang Lin, Umesh Adiga, Kathy Olson, John F. Guzowski, Carol A. Barnes, and Badrinath Roysam, “A Hybrid 3-D Watershed Algorithm Incorporating Gradient Cues & Object Models for Automatic Segmentation of Nuclei in Confocal Image Stacks,” Vol. 56A, No. 1, pp. 23-36 Cytometry Part A, November 2003. (pdf)
  41. Stewart, C. V., Tsai, C-L, and Roysam, B., “A Dual Bootstrap Iterative Closest Point (ICP) Algorithm: Application to Retinal Image Registration,” IEEE Transactions on Medical Imaging, Special Issue on Medical Image Registration, Vol. 22, No. 11, November 2003. (pdf)
  42. Michael S. Gee, Sosina Makonnen, Khalid al-Kofahi, Badri Roysam, Faribourz Payvandi, Hon-Wah Man, George W. Muller, and William M. F. Lee, “Selective Cytokine Inhibitory Drugs with Enhanced Antiangiogenic Activity Control Tumor Growth through Vascular Inhibition,” Cancer Research 63, 8073–8078, December 1, 2003. (pdf)
  43. Khalid Al-Kofahi, Ali Can, Sharie Lasek , Donald Szarowski, Natalie Dowell, William Shain, James N. Turner, Badrinath Roysam, “Median Based Robust Algorithms for Tracing Neurons from Noisy Confocal Microscope Images,” IEEE Transactions on Information Technology In Biomedicine, Vol. 7, No. 4, December 2003. (pdf)
  44. Lin, G., Fritzsche, K. L., Stewart, C. V., Tanenbaum, H. L., and Roysam, B., “Predictive Scheduling Algorithms for Real-time Feature Extraction and Spatial Referencing: Application to Retinal Image Sequences,” IEEE Transactions on Biomedical Engineering, Vol. 51, No. 1, January 2004. (pdf)
  45. Tsai, Chia-Ling, Stewart, Charles V., Tanenbaum, H. L., and Roysam, B., “Model-Based Method for Improving The Accuracy and Repeatability of Estimating Vascular Bifurcations and Crossovers From Retinal Fundus Images,” IEEE Transactions on IT for Biomedicine, vol. 8, No. 2, June 2004. (pdf)
  46. James Alexander Tyrrell, Justin LaPre, Christopher Carothers, Badrinath Roysam, and Charles V. Stewart, “Efficient Migration of Complex Off-Line Computer Vision Software to Real-Time System Implementation on Generic Computer Hardware,” IEEE Trans. on IT in Biomedicine, vol. 8, no. 2, June 2004. (pdf)
  47. Monica K. Chawla, Gang Lin, Kathy Olson, Almira Vazdarjanova, S. N. Burke, B. L. McNaughton, P. F. Worley, John F. Guzowski, Badrinath Roysam and  C. A. Barnes, “3D-catFISH: A System for Automated Quantitative Three-Dimensional Compartmental Analysis of Temporal Gene Transcription Activity Imaged by Fluorescence in situ Hybridization,” Journal of Neuroscience Methods, 139,  13–24, 2004. (pdf)
  48. Dowell-Mesfin, N. M., Abdul-Karim, M.-A., Turner, A.M.P., Schanz, S., Craighead, H.G., Roysam, B., Turner, J.N. and Shain, W. Topographically modified surfaces affect orientation and growth of Hippocampal neurons. J. Neural Engineering, UK Institute of Physics Publishing, 1:78–90, 2004. (pdf)
  49. Vijay Mahadevan, Harihar Narasimha Iyer, Badrinath Roysam, Howard L. Tanenbaum, “Robust Model-Based Vasculature Detection in Noisy Biomedical Images,” IEEE Transactions of IT in Biomedicine, vol. 8, no. 3, September 2004. (pdf)
  50. C. M. Warner, J. A. Newmark, M. Comiskey, S. R. De Fazio, D. M. O’Malley, M. Rajadhyaksha, D. J. Townsend, S. McKnight, B. Roysam, P. J. Dwyer, and C. A. DiMarzio, “Genetics and imaging to assess oocyte and preimplantation embryo health,” Journal of Reproduction, Fertility and Development, CSIRO Publishing, Victoria, Australia, vol. 16, pp. 729-741, 2004. (pdf)
  51. Richard J. Radke, Srinivas Andra, Omar Al-Kofahi, and Badrinath Roysam, “Image Change Detection Algorithms: A Systematic Survey,” vol. 14, No. 3, IEEE Transactions on Image Processing, March 2004. (pdf)
  52. Gang Lin, Monica Chawla, Kathy Olson, John F. Guzowski, Carol A. Barnes, and Badrinath Roysam, “Hierarchical, Model-based Merging of Multiple Fragments for Improved 3-D Segmentation of Nuclei,” Cytometry Part A, 63A:20-33, 2005. (pdf)
  53. G Lin, CS Bjornsson, KL Smith, MA Abdul-Karim, JN Turner, W Shain, B Roysam.  Automated Image Analysis Methods for 3D Quantification of the Neurovascular Unit from Multi-channel Confocal Microscope Images. Cytometry A, Vol. 66, No. 1, July 2005. (pdf)
  54. Harihar Narasimha-Iyer, James M Beach, Bahram Khoobehi, Hiroyuki Kawano and Badrinath Roysam, "Algorithms for Automated Oximetry over the Retinal Vascular Tree from Dual-Wavelength Fundus Images," Journal of Biomedical Optics, Vol. 10, No. 5, September/October 2005. (pdf)
  55. JA Tyrrell, V Mahadevan, R Tong, B Roysam, EB Brown, RK Jain, “3-D model-based complexity analysis of tumor microvasculature from in vivo multiphoton confocal images”, vol. 70, pp. 165-178, J. of Microvascular Research, 2005.
  56. Muhammad-Amri Abdul-Karim, Badrinath Roysam, Natalie Dowell, Andreas Jeromin, Murat Yuksel, Shivkumar Kalyanaraman, "Automatic Selection of Parameters for Vessel/Neurite Segmentation Algorithms", IEEE-Transactions on Image Processing, Vol. 14, No. 9, pp. 1338, September 2005. (pdf)
  57. John F. Guzowski, Jerilyn A. Timlin, Badri Roysam, Bruce L. Mc Naughton, Paul F. Worley and Carol A. Barnes, “Mapping Behaviorally Relevant Neural Circuits With Immediate Early gene Expression,” Current Opinion in Neurobiology, Vol 15, Issue 5, 2005 (pdf).
  58. O. Al-Kofahi, R.J. Radke, B. Roysam, and G. Banker, “Object-Level Analysis of Changes in Biomedical Image Sequences: Application to Automated Inspection of Neurons in Culture”, vol. 53, no. 6, IEEE Transactions on Biomedical Engineering, June 2006. (pdf)
  59. Harihar Narasimha-Iyer, Ali Can, Badrinath Roysam, Charles V. Stewart, Howard L. Tanenbaum, Anna Majerovics,  Hanumant Singh, “Robust detection and classification of longitudinal changes in color retinal fundus images for monitoring diabetic retinopathy,” Volume 53,  Issue 6,  Page(s):1084 – 1098, June 2006. (pdf)
  60. Omar Al-Kofahi, Richard J. Radke, Susan K. Goderie, Qin Shen, Sally Temple and Badrinath Roysam, “Automated cell lineage tracing: a method to analyze cell proliferative behavior developed using mouse neural stem cells,” Cell Cycle, vol. 5, No. 3, February 2006. (pdf)
  61. Bjornsson, CS, Oh, SJ, Al-Kofahi, YA, Lim, YJ, Smith, KL, Turner, JN, De, S, Roysam, B, Shain, W, Kim, SJ., “Shape- and insertion rate dependent tissue damage due to neuroprosthetic device insertion,” J. Neural Engineering, vol. 3, pp. 196-207, 2006.
  62. PoKman Chan, Tony Yuen, Badrinath Roysam, and Stuart C Sealfon, “Development of multiplex immunohistochemistry and in situ hybridization using colloidal quantum dots for semi-automated neuronal expression mapping in brain,” Proceedings of the International Society for Optical Engineering (SPIE), Colloidal Quantum Dots for Biomedical Applications, Marek Osinski, Kenji Yamamoto, Thomas M. Jovin (Editors), Vol. 6096, March 27, 2006.
  63. Harihar Narasimha-Iyer, Ali Can, Badrinath Roysam, Howard L. Tanenbaum and Anna Majerovics, "Integrated Analysis of Vascular and Non-Vascular Changes from Color Retinal Fundus Image Sequences," IEEE Trans Biomed Eng. 2007 Aug;54(8):1436-45.
  64. Harihar Narasimha-Iyer, James M Beach, Bahram Khoobehi and Badrinath Roysam, "Automatic Identification of Retinal Arteries and Veins from Dual-Wavelength Images using Structural and Functional Features", Volume: 54,  No. 8, pp. 1427-1435, IEEE Transactions on Biomedical Engineering Aug. 2007
  65. Frederique Ruf, Fernand Hayot, Myung-June Park, Gang Lin, Badrinath Roysam, Yongchao Ge, and Stuart C Sealfon, “Mixed Analog/Digital Gonadotrope Biosynthetic Response to Gonadotropin Releasing Hormone,” J. Biol. Chem., Vol. 281, Issue 41, 30967-30978, October 13, 2006.
  66. Nicolas Roussel, Christine A. Morton, Fern P. Finger, Badrinath Roysam, “A Computational Model for C. elegans Locomotory Behavior: Application to Multi-Worm Tracking,” IEEE Trans Biomed Eng. 2007 Oct;54(10):1786-97.
  67. Gang Lin, Monica K. Chawla, Kathy Olson, Carol A. Barnes, John F. Guzowski, and Badrinath Roysam, “A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei in 3D Confocal Microscope Images,” Volume 71A, Issue 9  , Pages 724 – 736, Cytometry, August 2007.
  68. Vicki L Sutherland, Jerilyn A Timlin, Linda T Nieman, John F Guzowski, Monica K Chawla, Paul F Worley, Badri Roysam, Bruce L McNaughton, Michael B Sinclair, Carol A Barnes, “Advanced Imaging of Multiple mRNAs in Brain Tissue using a Custom Hyperspectral Imager and Multivariate Curve Resolution,” Journal of Neuroscience Methods, 15;160(1):144-8, Feb 2007.
  69. James Alexander Tyrrell, Emmanuelle di Tomaso, Danel Fuja, Ricky Tong, Kevin Kozak, Edward B. Brown, Rakesh Jain, Badrinath Roysam, “Robust 3-D Modeling of Vasculature Imagery Using Superellipsoids,” vol. 26, no. 2, pp. 223-237,  IEEE Transactions on Medical Imaging, Feb 2007.
  70. Harihar Narasimha-Iyer, Vijay Mahadevan, James M Beach, Badrinath Roysam, “Improved Detection of the Central Reflex in Retinal Vessels Using a Generalized Dual Gaussian Model and Robust Hypothesis Testing,”May;12(3):406-10 IEEE Transactions on IT in Biomedicine, 2008.
  71. Frederique Ruf, Fernand Hayot, Myung-June Park,  Yongchao Ge, Gang Lin, Badrinath Roysam, and Stuart C Sealfon, “Noise Propagation and Scaling in Regulation of Gonadotrope Biosynthesis,” Biophys J. 2007 Aug 24; [Epub ahead of print].
  72. Yousef Al-Kofahi, Natalie Dowell-Mesfin, Christopher Pace, William Shain, James N Turner, Badrinath Roysam, Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images. Cytometry A. 2008 Jan;73(1):36-43.
  73. Christopher S Bjornsson, Gang Lin, Yousef Al-Kofahi, Arunachalam Narayanaswamy, Karen L Smith, William Shain, Badrinath Roysam. “Associative image analysis: a method for automated quantification of 3D multi-parameter images of brain tissue,” May 15;170(1):165-78) J. Neurosci. Methods, 2008.
  74. Chia-Ling Tsai, Benjamin Madore, Matthew Leotta, Michal Sofka, Gehua Yang, Anna Majerovics, Howard L. Tanenbaum, Charles V. Stewart, and Badrinath Roysam, "Automated Retinal Image Analysis over the Internet", IEEE Transactions on Information Technology in Biomedicine, Jul;12(4):480-77, 2008.
  75. Padfield D, Rittscher J, Thomas N, Roysam B. Spatio-temporal cell cycle phase analysis using level sets and fast marching methods. Med Image Anal. Jul 23, 2008 .
  76. Shen Q, Wang Y, Kokovay E, Lin G, Chuang SM, Goderie SK, Roysam B, Temple S. Adult SVZ stem cells lie in a vascular niche: a quantitative analysis of niche cell-cell interactions. Cell Stem Cell. Sep 11;3(3):289-300, 2008 .
  77. Jun SB, Hynd MR, Dowell-Mesfin NM, Al-Kofahi Y, Roysam B, Shain W, Kim SJ. Modulation of cultured neural networks using neurotrophin release from hydrogel-coated microelectrode arrays. J Neural Eng.  Jun;5(2):203-13, 2008.
  78. Ying Chen, Ena Ladi, Paul Herzmark, Ellen Robey, and Badrinath Roysam, Automated 5-D Analysis of Cell Migration and Interaction in the Thymic Cortex from Time-lapse Sequences of 3-D Multi-channel Multi-photon Images, Journal of Immunological Methods (accepted & in press), 2008.
  79. Ena Ladi, Tanja Schwickert, Tatyana Chtanova, Ying Chen, Paul Herzmark, Xinye Yin, Holly Aaron, Shiao Wei Chan, Martin Lipp, Badrinath Roysam and Ellen A. Robey, “Thymocyte-dendritic cell interactions near sources of CCR7 ligands in the thymic cortex,” Journal of Immunology (accepted & in press), 2008.

BOOK CHAPTERS

1.       Holmes, T. J., Bhattacharyya, S., Cooper, J. A., Hanzel, D., Krishnamurthi, V., Lin, W., Roysam, B., Szarowski, D. H., and Turner, J. N., “Light Microscopic Images Reconstructed by Maximum Likelihood Deconvolution,” Handbook of Confocal Microscopy, J. Pawley (ed.), Plenum Press, New York, 1995.

2.       Kenneth H. Fritzsche, Ali Can , Hong Shen , Charlene Tsai , James N. Turner, Howard L. Tanenbaum , Charles V. Stewart , Badrinath Roysam , “Automated Model Based Segmentation, Tracing, and Analysis of Retinal Vasculature from Digital Fundus Images” Chapter in Angiography and Plaque Imaging: Advanced Segmentation Methods,, Jasjit S. Suri and Swami Laxminarayan (eds.), pp. 225-298, ISBN 0-8493-1740-1, CRC Press, Boca Raton, FL , This book is part of the Biomedical Engineering Series edited by Michael Neuman, 2003.

3.       Jasjit S. Suri, Sameer Singh, Swamy Laxminarayan, Roberto M. Cesar Jr., Herbert F. Jelinek, Petia Reveda, Badrinath Roysam, Charles V. Stewart, Kenneth H. Fritzsche, James Williams and Huseyin Tek, “A Note on Future Research in Vascular and Plaque Segmentation,” Chapter in Angiography and Plaque Imaging: Advanced Segmentation Methods,, Jasjit S. Suri and Swami Laxminarayan (eds.), pp. 501-521, ISBN 0-8493-1740-1, CRC Press, Boca Raton, FL , This book is part of the Biomedical Engineering Series edited by Michael Neuman, 2003.

4.       Badrinath Roysam, Gang Lin, Muhammad-Amri Abdul-Karim, Omar Al-Kofahi, Khalid Al-Kofahi, William Shain, Donald H. Szarowski, James N. Turner, “Automated 3-D Image Analysis Methods for Confocal Microscopy,” Handbook of Confocal Microscopy, Chapter 15, pp. 316-337, Third Edition, James Pawley (ed.), Springer, New York, January 2006.

5.       Kenneth H. Fritzsche, Charles V. Stewart, Badrinath Roysam, “Determining Retinal Vessel Widths and Detection of Width Changes,” in Automated Detection of Retinal Pathology, Herbert Jelinek & Michael J. Cree  (eds.),Taylor and Francis Group, (to appear) 2007/2008.

6.       Badrinath Roysam, Gang Lin, Christopher Bjornsson, Arun narayanaswamy, Ying Chen, William Shain, William Mohler, Ellen Robey, “The FARSIGHT Project: Associative Multi-dimensional Image Analysis Methods for Optical Microscopy,” invited submission to “Microscopic Image Analysis for Life Science Applications" Eds. Jens Rittscher, Raghu Machiraju, & Steve Wong, Artech Publishing House, 2008.

7.       Dirk Padfield, Jens Rittscher, Nick Thomas, and Badrinath Roysam. Microscopic Image Analysis for Life Science Applications, chapter 13. Artech Publishing House, 2008.

BOOK REVIEWS

Roysam, B., Review of: Computational Vision by Harry Wechsler, SIAM Review, Vol. 35, No. 1, pp. 165-166, March 1993.

IEEE INSTRUCTIONAL VIDEO

IEEE video tutorial lecture: “Parallel Image Processing Technology”, 7 hrs, 1992. ISBN 0-7803-0362-8, Sponsored by the IEEE Educational Activities Board.

CONFERENCE PUBLICATIONS

**Note: Asterisks highlight award-winning papers

  1. Miller, M. I., Larson, K. B., Saffitz, J. E., Snyder, D. L., Thomas Jr., L.J., and Roysam, B., "A New Method for Analysis of Electron Microscopic Autoradiographs," abstract, Proceedings of the 1985 Cell Biology Conference, Atlanta, GA, 101(5), pt. 2:85a, 1985.
  2. Miller, M. I., B. Roysam, J. E. Saffitz, K. B. Larson, and L. J. Thomas Jr., "Validation of Maximum-likelihood Analysis of Electron Microscopic Autoradiographs," 70th Annual Meeting, FASEB, vol. G-22 II, 1844, April 1986.
  3. Miller, M. I., Roysam, B., Saffitz, J. E., Larson, K. B. , Snyder, D. L., and Thomas, Jr., L. J., "A New Method for the Analysis of EM Autoradiographs," 3rd International Symposium on Autoradiography, Sheffield University, Sheffield, England, September 16-18, 1986.
  4. Roysam, B., J. A. Shrauner, and M. I. Miller, "Bayesian Imaging Using Good's Roughness Measure-Implementation on a Massively Parallel Processor," International Conference on Acoustics, Speech and Signal Processing, IEEE, New York, March 1988.
  5. Miller, M.I., B. Roysam, K. R. Smith, and J. T. Udding, "Mapping Rule-Based Regular Grammars to Gibbs' Distributions," AMS-IMS-SIAM Joint Conference on Spatial Statistics and Imaging, American Mathematical Society, July 1988.
  6. Roysam, B. and M. I. Miller, "Mapping Deterministic Rules to Stochastic Representations via Gibbs Distributions on Massively Parallel Analog Networks: Application to Global Optimization," Proceedings of the 1988 Connectionist Models Summer School (eds. David Touretzky, Geoffrey Hinton, Terrence Sejnowski), pp. 229-238, Carnegie Mellon University, Pittsburgh. Morgan Kaufmann Publishers, June 1988.
  7. **Roysam, B., "A New Method for EM Autoradiography: Evaluation and Comparison to Crossfire Analysis," Proceedings, Electron Microscopy Society of America (ed. G. W. Bailey), pp. 844-845, August 1988. (Presidential Student Award)
  8. Roysam, B., "A New Method for EM Autoradiography: Small System Implementation Technique," Proceedings, Electron Microscopy Society of America (ed. G. W. Bailey), August 1988.
  9. Roysam, B. and M. I. Miller, "Grammars and Bayes' Priors for Hierarchical Image Processing on Massively Parallel Processors," Proceedings, 26th Allerton Conference on Communication, Control and Computing, University of Illinois at Urbana-Champaign, Monticello, IL, October 1988.
  10. Smith, K. R., M. I. Miller, and B. Roysam, "Representing Regular Grammars on Massively Parallel Processors via a Cellular Automata Programming Model," Frontiers of Massively Parallel Computation, NASA, IEEE, Fairfax, Virginia, October 1988.
  11. Miller, M. I., B. Roysam, and K. R. Smith, "Mapping Rule-based and Stochastic Constraints to Connection Architectures: Implications for Hierarchical Image Processing," Proc. SPIE Conf. on Visual Communications and Image Processing, vol. 1001,part 2, pp. 1078-1085, Nov 1988.
  12. Roysam, B. and Michael I. Miller, "A Unified Approach for Hierarchical Imaging Based on Joint Hypothesis Testing and Parameter Estimation," IEEE Conference on Acoustics, Speech and Signal Processing, Glasgow, Scotland, U. K., May 1989.
  13. Smith, K. R., Roysam, B., and Miller, M. I., "Optimal Learning and Inference over MRF Models: Application to Computational Vision on Connectionist Architectures," Proc. IEEE Conference on Neural Information Processing Systems, November 1989, Morgan Kaufmann, Palo Alto, CA.
  14. Roysam, B., and Miller, M. I., "Stochastic Representation of Memoryless Boolean Functions: Application to Boundary Estimation at Low Contrast," IEEE-ICASSP, Albuquerque, April 1990.
  15. Miller, M. I., Maffitt, D. R., Shrauner, J. A., Roysam, B., Grenander, U., “Automated Segmentation of Biological Shapes in Electron Microscopic Autoradiography,” 1991 Conference on Information Sciences and Systems, Johns Hopkins University, Baltimore, Maryland, March 20-22 1991.
  16. Bhattacharjya, A. K. and Roysam, B., “A Modified Genetic Algorithm for Estimation of Translation and Rotation Without Correspondence: Parallel Implementation on the DAP-510 System," IEEE MDSP Workshop, Lake Placid, NY, September 1991.
  17. **Roysam B., Cohen, A., Getto, P., and Boyce, P., "Computational Visualization of Lighted Exit Signs Through Complex Smoke Media," 26th IEEE Conference on Industry Applications, October 1991. (Prize Paper Award)
  18. Roysam, B., C. Srinivas, J. N. Turner, "Unsupervised Noise Removal Algorithms For 3-D Confocal Fluorescence Microscopy," SPIE Proceedings Vol. 1660, No. 27, February 1992.
  19. Krishnamurthi, V., Roysam, B., Turner J. N., and Holmes, T. J., "Blind Deconvolution of 2-D and 3-D Fluorescent micrographs," SPIE Proceedings Vol. 1660, No. 13, February 1992.
  20. Willis, B. H., Roysam, B., Turner J. N., Holmes, T. J., "Algorithms for 3-D Brightfield Microscopy," SPIE Proceedings Vol. 1660, No. 14, February 1992.
  21. Holmes, T. J., Roysam, B., Turner, J. N., Krishnamurthi, V., Liu, Y. H., and Willis, B. H., “Image Reconstruction Methodologies for 2D and 3D Microscopy, 3D Imaging Sciences in Microscopy, Amsterdam, 1992. (Plenary talk)
  22. Turner, J. N., Holmes, T., and Roysam, B., “Applications of 3-D Light Microscopy to Neurobiology and some Improved Imaging Algorithms, (invited presentation) at Scanning ‘92, vol. 14, Supplement II, pp. 17-18, April 1, 1992.
  23. Chishti, M. A., Seegal, R. F., Turner, J. N., Roysam, B., and Ancin, H., “Automated Counting of Dopaminergic Neurons in the Substantia Nigra of Rats using Laser-Scanning Confocal Microscope,” The Toxicologist: Proceedings of the Annual Meeting of the Society of Toxicology, New Orleans, March 14-18, vol. 13, pp. 209, 1993.
  24. McMurdy, R. K., and Roysam, B., “Improving RAID-5 Performance by Un-Striping Moderate-Sized Files,” Proc. 22nd International Conference on Parallel Processing, Session 11B, St. Charles, IL, August 16-20, 1993.
  25. Roysam, B., Bhattacharjya, A. K., Ancin, H., Cohen, A. R., Mackin, R. W., Becker, D. E., and Rodriguez, C., “Intelligent Computational 3-D Microscopy: New Results in Segmentation, Noise Removal, Cell Counting and Automated Neuron Tracing,” Invited presentation, Proceedings Fifty-First Annual Meeting of the Microscopy Society of America, (G. W. Bailey and C. L. Reider eds.) pp.160-161, San Francisco Press, 1993.
  26. Turner, J. N., Szarowski, D. H., Lin, W., Ancin, H., Cohen, A., and Roysam, B., “3-D Imaging and Image Reconstruction Applications in Neurobiology,” Invited presentation, Proceedings of Scanning ‘93, Vol. 15, Supplement III, pp. 65-67, Orlando, FL, April 21-23, 1993.
  27. Lin, W., Holmes, T. J., Ancin, H., Roysam, B., Szarowski, D. H., and Turner, J. N., “Three-Dimensional Light Microscopy, Optimized Staining and Automated Image Analysis of Cell Nuclei in Thick Slices,” Proceedings Fifty-First Annual Meeting of the Microscopy Society of America, (G. W. Bailey and C. L. Reider eds.) pp.268-269, San Francisco Press, 1993.
  28. **Ancin, H., and Roysam, B., “Automated 3-D Cell Population Analysis in Thick Tissue Sections from Laser-Scanning Confocal Microscopy Data,” Proceedings Fifty-First Annual Meeting of the Microscopy Society of America, (G. W. Bailey and C. L. Reider eds.) pp.268-269, San Francisco Press, 1993. (Presidential Student Award)
  29. Bhattacharjya, A. K., and Roysam, B., Joint Solution of Low, Intermediate and High-Level Vision Tasks by Global Optimization: Application to Computer Vision at Low SNR,” Proceedings of the 1993 Connectionist Models Summer School, (Eds: Mozer, M. C., Smolensky, P., Touretzky, D. S., Elman, J. L., and Weigend, A. S.), pp. 39-47, Hillsdale, NJ: Erlbaum Associates, 1994.
  30. Seegal, R. F., Chishti, M. A., Turner, J. N., Roysam, B., and Ancin, H., “PCBs Reduce the Number of Dopaminergic Neurons in Rat Substantia Nigra Determined by Laser-Scanning Confocal Microscopy,” The Toxicologist: Proceedings of the Annual Meeting of the Society of Toxicology, Dallas, Texas, vol. 14, pp. 353, 13-17 March, 1994.
  31. Holmes, T. J., Bhattacharyya, S., Cooper, J. A., Hanzel, D., Krishnamurthi, V., Lin, W., Roysam, B., Szarowski, D., Turner, J. N., "Blind Deconvolution for 3D Deblurring in Transmitted Light, Widefield Fluorescence, and Confocal Microscopy," International Conference on 3D Imaging Science in Microscopy, Munich, April 25-28, 1994.
  32. Ancin, H., Roysam, B., Chestnut, M. H., Otte, T. E., Szarowski, D. H., and Turner, J. N., “Automated Counting and 3-D Morphometry of Nuclei in Thick Tissue Slices from Laser-Scanning Confocal Microscopy Data,” Proceedings of the 52nd Annual Meeting of the Microscopy Society of America, G. W. Bailey and A. J. Garratt - Reid (eds.), pp. 222-223, August 1994.
  33. Becker, D. E., Ancin, H., Roysam, B., and Turner, J. N., “Fast Automated Mosaic Synthesis Method for 2-D/3-D Image Analysis of Specime