Image processing engineer

Dr. Umesh Adiga (US Citizen)

****, ********* ***** #***

Loveland, OH45140

*****.*****@*****.***

513-***-**** (cell)

I am a senior Image Processing Engineer with eleven years of post-PhD experience in algorithm and systems development for image processing, computer vision and pattern recognition applications. Although much of my work is concentrated in automation of image data analysis for life sciences and medical sciences, I have also worked in defense and security related applications development. Have worked in academic, govt. R&D labs and industrial R&D in several countries (America, Europe, Asia...).

My goal is to successfully lead a group of engineers and scientists or work as a part of a team in exploring, design and development of next generation technology for complete automation of image and signal processing systems in the advanced technology and national security fields.

Experience (Engineering and Technology):

Industrial Engineering R&D:

1. Senior Engineer (Image Analytics and Pattern Recognition): UES Inc., a defense contract company, Dayton, Ohio. (2009-till date)

• Time lapse phase contrast data and multi-channel image analysis system development for timely recognition and defense against biochemical threats

• Have completed development of multi spectral 4D cell image data (both phase contrast image analysis and stained image analysis) segmentation, labeling followed by extraction of over 10,000 features per cell to build connectivity maps between chemical treatment, siRNA knockout and Targetron in a large scale host-pathogen Interactome project.

• Imaging live and fixed cells in 384 well micro plates using high content and high throughput imaging systems.

• Automatic exploratory informatics software development

2. Senior Image Processing Engineer: Ikonisys Inc. New Haven, CT (2008-2009)

• High content and high throughput bio and pathological data analysis

• Circulating tumor cell detection (Segmentation, antibody based feature analysis)

• Cervical fetal cell detection (Segmentation, FISH based feature analysis)

• Feature analysis (Morphological, texture, frequency domain) of cervical specimens and antibody expressions for cancer cell detection

• Model based accurate detection of FISH signals

3. Lead Computer Scientist/Engineer: General Electric Global Research, (Imaging Technologies), (2006-2008)

• Pulmonary Emboli detection in lung CT (Tech. Lead; Patents with GE)

• Real time analysis of left ventricle orientation in MRI (part of the one touch cardiac project; technology developer; Patents with GE)

• Software development for CT Perfusion image analysis for stroke (Initiative and Tech. Lead)

• Applications development for dual energy CT (Patents application pending with GE).

• Digital pathology: Towards quantifying architectural changes in the tissue (Initiative and Tech Lead).

• Zebrafish Analysis Tool Development (Initiative and Tech. Lead; Patents with GE)

• Tumor margin characterization for dye quality analysis (Software Development Tech Lead; Patents with GE)

• Tomosynthesis based threat detection for security

• Auto-pilot software for locomotives (Tech. lead; Patent application is pending with GE)

• Video anti piracy software development (project member, software design and development)

• Vehicle detection in aerial images of an occluded environment (Lokheed project; Design and development)

Govt. R&D Lab:

4. Computer Scientist: Lawrence Berkeley National Laboratory, Berkeley, California, USA, 2002-2006 (including postdoc duration at LBNL).

• Electron microscopy image analysis for characterizing pathologically important variations (project initiation and Tech. lead)

• Particle picking and quality indexing for single particle reconstruction (Tech. lead)

• Algorithm design and software development for multi-spectral breast cancer image data.

• Project initiation to explore the correlation between initial genetic variation and successive histological changes in cancer development based on 3D data obtained by confocal microscopy.

Academic:

5. Postdoctoral Research Associate: University of Arizona (Neural Systems Memory and Aging) and Rensselaer Polytechnic Institute (ECSE), USA, June 2001 – Jan 2002.

• Design, development of automated image analysis software for functional analysis of the hippocampus activity at sub-cellular resolution (patent with RPI)

6. Postdoctoral Research Scientist: Oxford University, (Wellcome Trust Centre for Human Genetics), UK, Oct 1999 – June 2001.

• Design and development of signal processing software to reduce error in reading the allele sizes in human genetics research

• Design and development of image analysis software for differentiating heterozygous and homozygous alleles in gel plate runs.

7. Guest Scientist: Institute for Health and Environmental Research, GSF, Munich, Germany, 1996-1997.

• Design and development of FISH characterization and counting/cell-nuclei in 3D images of tissue specimens to analyze genetic variation in prostate cancer.

8. Lecturer: Kalpataru Institute of Technology, Bangalore University) India, Jul 1993- Oct 1994

Internship:

9. Engineer Trainee, Philips, Bombay, India during 1989 and 1990-91.

Computing: C, C++, C#, MATLAB, IDL; .NET (MS-Windows, Visual Studio), Linux and Unix platforms. Beginner level of ASP.NET applications with C#.

Education:

1. Ph. D. (Image Processing and Pattern Recognition) Indian Statistical Institute, 94-99. Thesis: Design and development of a quantitative evaluation system for the 3D images of prostate cancer tissue obtained using multi-spectral confocal imaging.

2. M. Sc. (Computer Science), Lincoln College, Oxford University, UK.

3. M. E. (Electronics) Marathwada University, India.

4. B. E. (Electronics & Communication.) Mysore University, India.

Scholarships and Fellowships:

1. Postdoctoral Research Fellowship, Lawrence Berkeley National Laboratory, (Jan 2002 – May2005),

2. Postdoctoral Research Associate Fellowship University of Arizona, 2001,

3. Postdoctoral Scholarship (Visiting), Rensselaer Polytechnic Institute, 2001,

4. Wellcome-Trust Postdoctoral Fellowship, Oxford University, 1999-2001,

5. Wellcome-Trust scholarship, Oxford University, 2000-2001,

6. Senior Research Fellowship Indian Statistical Institute, 1996-1999,

7. Guest Scientist Research Fellowship, GSF-Munich, Germany, 1996-1997,

8. Junior Research Fellowship Indian Statistical Institute, 1994-1996,

9. Graduate Aptitude Test for Engineering (GATE) Scholarship, 1991-1993.

Reviewer of articles in journals such as:

1. IEEE Trans. on Biomedical Engineering, 2. IEEE Trans. on Information Technology In Biomedicine, 3. Image and Vision Computing, 4. Cytometry, 5. J. of Biomolecular Screening

Invited Speaker:

1. Institute of Pathology, GSF-National Research center for Health and Environment, Munich, Germany.

2. School of Computer Science, Monash University, Melbourne, Australia.

3. German Cancer Research Center, BKFZ, Heidelberg, Germany.

4. Computer Vision group, EECS, University of California at Berkeley, USA.

5. Cancer Research Center, University of California at San Francesco, USA.

Products/Patents/Disclosures (after joining General Electric Company in 2006):

Products:

1. Automatic quantification of tumor margin for dye development and surgery (GE Patent Application 229637-1 (GERD:0887) )

2. One touch cardiac (patent applied; US Application number: US 12/323594)

3. Defocus detection (International patent application # PCT/SE2009/050623)

4. Pulmonary emboli detection (European patent # 11152643.0 - 2218)

5. Automatic detection of rail-tracks (possible patent; in GE docket)

6. Multispectral Confocal Data Analysis Tool (Patented and productized by RPI)

7. System for automatic bright-field image analysis (under consideration for patent by AFRL)

Patents Disclosures (2006 – till date):

A few more trade-secret algorith/software in CTC detection, infectious disease analyses, video analysis (2009-2011).

Publications (mostly based on academic work):

In Journals

1. Umesh Adiga, Debbie Taylor, Brian Bell, Larissa Ponomareva, Thomas J. Lamkin, Phenotypic grouping of the macrophages during 72 hour infection period using image analytics, to be in preparation for submission to IEEE Trans. On Biomedical Engineering, 2011.

2. Umesh Adiga, Debbie Taylor, Brian Bell, Larissa Ponomareva, Stephen Kanzlemar, Ryan Kramer, Sandra Nelson, Thomas J. Lamkin, Automated Analysis and Classification of Infected Macrophages using Bright-field Amplitude Contrast Data, submitted to J. of Biomolecular Screening, 2011.

3. Wah Chiu, Chao Yang, Wen Jiang, Donghua Chen, Esmong Ng, Umesh Adiga, “Estimating Contrast Transfer Function and associated Parameters by Constrained Nonlinear Optimization”, J. of Microscopy, Vol. 233, pp. 391-403, 2009.

4. Umesh Adiga, Malladi R., Gonzalez R.F., Solorzano C.O., “A robust methodology for the analysis of breast cancer tissue blocks”, IEEE Trans. on Image Processing, Vol. 15, Issue 8, 2006.

5. Umesh Adiga, William Baxter, Bimal Rath, Beate Rockel, Richard Hall, Jochim Frank, Robert Glaeser, “Particle picking by segmentation: A comparative study with SPIDER based manual particle picking”, J. of Structural Biology, vol. 152, Issue 3, pp. 211-220, 2005.

6. Umesh Adiga, R. Malladi, W. Baxter, RM Glaeser, “A Binary Segmentation Approach for Boxing Ribosome Particles in Cryo Micrographs”, J. of Structural Biology, Vol. 145, pp. 142-151, 2004.

7. Gang Lin, Umesh Adiga, Jon Guzawski, Kathy Olson, Carol Barnes, Badri Roysam, “A Hybrid 3D Watershed Algorithm Incorporating Gradient cues and Object Models for Automatic Segmentation of Nuclei in Confocal Image Stacks” Int. J. of Cytometry, Vol. 56A, pp. 23-36, 2003 (Patented by RPI).

8. Umesh Adiga and Jonathan Flint, “An Efficient Tool for Genetic Experiments: Agarose Gel Image Analysis”, Pattern Recognition Vol. 36, pp. 2453-2461, 2003.

9. Umesh Adiga, “Segmentation of Volumetric Tissue Images using constrained active models,” J. Computer Methods and Programs in Biomedicine, Vol. 71, pp. 91-104, 2002.

10. Umesh Adiga, “An Integrated System for Feature Evaluation of 3-D Images of a Tissue Specimen,” J. Analytical Cellular Pathology, Vol. 24, pp. 47-58, 2002.

11. Umesh Adiga, “An integrated approach for segmentation of 3-D confocal images of a tissue specimen”, J. Microscopy Research and Techniques, Vol. 54, pp. 260-270, 2001.

12. Umesh Adiga and B. B. Chaudhuri, “An efficient method based on watershed and rule based merging for segmentation of 3-D histo-pathological images”, J. Pattern Recognition, Vol. 34/7, pp-1449-1458, 2001.

13. Umesh Adiga, A. Bhomra, MG. Turri, A. Nikod, S. Datta, P. Jeavons, R. Mott, J. Flint, "Automation of analysis of agarose gel images". J. Bioinformatics, Vol. 17, pp. 1084-1089, 2001.

14. Umesh Adiga, B. B. Chaudhuri, “Efficient methods for noise reduction and enhancement of confocal microscopy images”, J. MICRON, Vol. 32, pp. 363-370, 2001. Awarded an honorarium by the publisher.

15. Umesh Adiga, Sam JL Knight, and B. B. Chaudhuri, “Characterization and automatic counting of FISH signals in 3-D tissue images”, J. Image Analysis and Stereology, Vol. 20, No. 1, pp. 41-52, 2001.

16. Umesh Adiga, and B. B. Chaudhuri, “Region based techniques for segmentation of volumetric histo-pathological images”, J. Computer Methods and Programs in Bio-Medicine, Vol. 61, No. 1, pp. 23-47, 2000

17. Umesh Adiga and B. B. Chaudhuri, "Segmentation and counting of FISH signals in confocal microscopy images", J. MICRON, Vol. 31, No. 1, pp. 5-15, 2000.

18. Umesh Adiga and B. B. Chaudhuri “Deformable models for segmentation of CLSM images and its application in FISH signal analysis”, J. Analytical Cellular Pathology, Vol. 18, No. 4, pp. 211-225, 1999.

19. Umesh Adiga and B. B. Chaudhuri, "An efficient cell segmentation tool for confocal microscopy tissue images for quantitative evaluation of FISH signals", J. Microscopy Research and Techniques, Vol. 43, 1-20, 1998.

20. K. Rodenacker, M. Aubele, P. Hutzler and Umesh Adiga, “Groping for quantitative 3D image analysis: an Approach to Quantitative Evaluation of Fluorescence in situ Hybridization in thick tissue sections of prostate carcinoma", J. Analytical Cellular Pathology, Vol. 15, pp. 19-29, 1997.

21. Umesh Adiga and T. R. Sontakke, "Nuclear Magnetic Resonance Imaging - a Review", J. of Inst. of Engineers (India), Vol. 73, pp. 57-63, 1993.

In Conference Proceedings and posters:

22. Umesh Adiga, Debbie Taylor, Brian Bell, Larissa Ponomareva, Stephen Kanzlemar, Derek Tepe, Sandra Nelson, Thomas J. Lamkin, Modeling Phenotypic Changes in Macrophages Infected by Francesella, Poster presentation In Chemical and Biological defense science and technology conference, Orlando, Florida, 2010

23. Brian Bell, Umesh Adiga, Debbie Taylor, Larissa Ponomareva, Stephen Kanzlemar, Derek Tepe, Sandra Nelson, Thomas J. Lamkin, Real Time High Content Analysis of Bacterial infections of human monocyte derived macrophages, Poster presentation In Chemical and Biological defense science and technology conference, Orlando, Florida, 2010

24. Umesh Adiga, Daniel Blezek, “Automated Cardiac Short Axis Acquisition from a Free-breathing Non-gated FIESTA” Accepted for presentation in ISMRM 2007, Berlin, Germany.

25. Umesh Adiga, B.B. Chaudhuri and K. Rodenacker, "Semi-automatic segmentation of tissue cells from confocal microscopy images", In IEEE Proceedings of 13th Int. Conf. on Pattern Recognition, ICPR-96, 3, pp. 494-497, Vienna, Austria, 1996.

26. Umesh Adiga, and B. B. Chaudhuri, "Segmentation of histo-pathological images by surface following using constrained snakes", In IEEE Proceedings of 14th International Conference on Pattern Recognition, ICPR-98, pp. 1674-1676, Brisbane, Australia, 1998.

27. Umesh Adiga and B. B. Chaudhuri, "Analysis of volumetric images of filamentous bacteria in industrial sludge", In IEEE Proceedings of 14th International Conference on Pattern Recognition, ICPR-98, pp. 1735-1737, Brisbane, Australia, 1998.

28. Umesh Adiga and B. B. Chaudhuri, "Segmentation of 3-D histo-pathological images using snakes and its application in quantitative evaluation of FISH signal", In Proceedings of 2nd International Conference on Medical Image Understanding and Analysis, MIUA-98, Leeds, UK, 1998.

29. Umesh Adiga and B. B. Chaudhuri, "Automatic segmentation of 3-D cells from confocal microscopy images and its application in FISH signal evaluation", In Proceedings of 16th International CODATA Conference, CODATA-98, New Delhi, 1998.

30. Umesh Adiga and B. B. Chaudhuri, "Classification of prostate tumor specimen based on cytological and histological features measured from 3D images", In Proceedings of 16th International CODATA Conference, CODATA-98, New Delhi, 1998

31. Umesh Adiga and B. B. Chaudhuri, “Quantitative evaluation of bacteria in industrial sludge by 3-D image analysis", In Proceedings of 16th International CODATA Conference, CODATA-98, New Delhi, 1998.

32. Umesh Adiga and B. B. Chaudhuri, “Automatic prostate cancer grading system based on 3-D histo-pathological images", In Proceedings of IAPR workshop on Machine Vision and Applications, MVA-98, Chiba, Japan, 1998.

33. Umesh Adiga and B. B. Chaudhuri, “Active surfaces for the segmentation of the volumetric histo-pathological images”, In Proceedings of Indian Conf. on CVGIP, IIT, New Delhi, 1998, pp. 36-44.

34. Umesh Adiga and B. B. Chaudhuri, “Characterization and automatic counting of FISH signals in 3-D tissue images”, 10th International Congress on Stereology, Melbourne, Australia.

35. Umesh Adiga and B. B. Chaudhuri, “Watershed with rule based merging for efficient cell segmentation”, 10th International Congress on Stereology, Melbourne, Australia.

36. Saurabh Roy, Umesh Adiga, B. Roysam, “Quantitative Evaluation of Hippocampus Tissue for Functional Imaging”, ISAC - XXI International Congress of International Society for Analytical Cytology, 2002 (Student Award).

37. RF Gonzalez, Umesh Adiga, A. Idica, T. Deshcamps, R. Malladi, C. Ortiz de Solórzano, “Automatic segmentation of structures in normal and neoplastic mammary gland tissue sections”, SPIE Proceedings of Photonic West Conference, SanJose, California, 2003, pp. 4964-26

38. Umesh Adiga, R. Malladi, RM Glaeser, “Automated particle selection based on binary segmentation”, presented in Gordon Conference on Three-dimensional Electron Microscopy, New London, NH, USA, June 2003.

In Tech. Reports:

39. Umesh Adiga, R. Malladi, Robert M. Glaeser, “Extraction of Macromolecule Images from cryoEM Micrographs”, Technical Report No. LBNL-52387, Lawrence Berkeley National Laboratory, University of California, Berkeley, USA, 2003.

40. Umesh Adiga, R. Malladi, W. Baxter, RM Glaeser, “A Binary Segmentation Approach for Boxing Ribosome Particles in Cryo Micrographs”, Technical Report No. LBNL-52585, Lawrence Berkeley National Laboratory, University of California, Berkeley, USA, 2003.

41. Umesh Adiga, R. Malladi, “A Contour Based Approach for segmentation of particles in CryoEM”, Technical Report No. LBNL-53906, Lawrence Berkeley National Laboratory, University of California, Berkeley, USA, 2003.

42. Umesh Adiga, B. Roysam, and B.B. Chaudhuri, Segmentation of volumetric histological data obtained using confocal microscope: a review, LBNL-54478, 2003.

43. Umesh Adiga, Adam Idica, Rodrigo F Gonzalez, Carlos O Solorzano, “An Efficient Approach to Segmentation of Cell-nuclei in Tissue Images: Application to Breast Tissue Blocks”, Technical Report No. LBNL-54445, Lawrence Berkeley National Laboratory, University of California, Berkeley, USA, 2004.

In Theses:

44. B.E. thesis: Development of continuous heart beat rate monitor based on LDR, Mysore University, India, 1990.

45. M.E. thesis: Review of nuclear magnetic resonance imaging, Marathwada University, India, 1993.

46. M.S. thesis: Automation of agarose gel analysis, Oxford University, UK, 2001.

47. Ph.D. thesis: Quantitative evaluation of 3-D histo-pathological images obtained using confocal microscope, Indian Statistical Institute, India, 1999.

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