• ME, Computer Science and Engineering, Jadavpur University, Calcutta, India
• PhD, Computer Science, India Statistical Institute, Calcutta, India

Over the last two decades, Punam Saha, PhD, has been working on basic and translational research related to structural analysis in various medical applications including bone and pulmonary imaging. His research works led to the development of several technologies, including digital topological analysis, fuzzy distance approach, and tensor scale, which are being used at multiple research institutions and have been successfully applied to various research and clinical studies. His research group pioneered methodologies for the characterization of individual trabeculae on the continuum between perfect plates and perfect rods and highly accurate measures of trabecular bone thickness, spacing, and orientation. Recently, a fully automated algorithm has been developed and validated in his laboratory for cortical bone segmentation on in vivo images acquired using clinical computed tomography (CT) scanners. The quantitative bone structural metrics developed in his laboratory are currently being used at multiple research institutes in different clinical and research studies including:

1. Iowa Bone Development Study (University of Iowa (UI))
2. Cartilage, bone, and marrow interactions in knee osteoarthritis (New York University)
3. Bone improvement study in spinal cord injury patients (UI)
4. Bone studies among patients with cystic fibrosis, patients with anorexia nervosa, and patients with serotonin reuptake inhibitor intake (UI)

Besides research contributions to bone imaging, Dr. Saha's research group developed a technique to separate arterial and venous trees in non-contrast pulmonary CT using a novel multi-scale topo-morphologic opening at conjoining locations. Research contributions from his laboratory to several active medical imaging fields, including quantitative morphometry, skeletonization, segmentation, shape-analysis, and image registration are widely regarded within the biomedical imaging community. He has served as the Principal Investigator of one NIH R01 grant, and is currently serving as the subcontract PI of two NIH consortium R01 grants and Co-I of several NIH R01 grants, related to in vivo assessment of bone strength and fracture risk. In summary, his research experience in the area of in vivo TB micro-architectural assessment together with enthusiastic support from several investigators at the University of Iowa and at the National Jewish Health will be productive and will lead to a successful performance of the proposed study.

During Dr. Saha's PhD research, he pioneered the theory and algorithms of digital topology and geometry enabling local characterization of surfaces, curves, and their junctions and edges. Also, he developed the algorithm for segmentation of multiple structures glued at junctions. At the Laboratory of Structural NMR Imaging, University of Pennsylvania, he applied the theory and algorithms of digital topological analysis to characterize individual trabecular plates (surfaces) and rods (curves) at in vivo MR imaging. Also, the theory and algorithms were adopted for individual trabecular segmentation and plate/rod classification. Currently, these methods are being used at several universities, including the University of Pennsylvania, Columbia University, and New York University. Recently, his research team has developed a new theory and algorithm that enables measuring individual trabecular plate-width in the unit of microns and allows the classification of individual trabeculae on the continuum between a perfect plate and a perfect rod.

1. P.K. Saha and B.B. Chaudhuri (1996). 3D Digital topology under binary transformation with applications. Computer Vision and Image Understanding 63: 418-429
2. P.K. Saha, B.R. Gomberg, and F.W. Wehrli (2000). Three-dimensional digital topological characterization of cancellous bone architecture. International Journal of Imaging Systems and Technology 11:81-90
3. P.K. Saha, Y. Xu, H. Duan, A. Heiner, and G. Liang (2010). Volumetric topological analysis: a novel approach for trabecular bone classification on the continuum between plates and rods. IEEE Transactions on Medical Imaging 29:1821-1838
4. P.K. Saha, Y. Liu, C. Cheng, D. Jin, E.M. Letuchy, Z. Xu, R.E. Amelon, T.L. Burns, J.C. Torner, S.M. Levy, and C.A. Calarge(2015, accepted). Characterization of trabecular bone plate-rod micro-architecture using multi-row detector CT and the tensor scale: algorithms, validation, and applications to pilot human studies. Med Phy.

Dr. Saha's research group has developed a highly accurate algorithm to compute trabecular bone thickness and spacing that accounts for partially occupied bone voxels and eliminates digital grid effects.

1. P.K. Saha, F.W. Wehrli, and B.R. Gomberg (2002). Fuzzy distance transform-theory, algorithms, and applications. Computer Vision and Image Understanding 86:171-190
2. P.K. Saha and F.W. Wehrli (2004). Measurement of trabecular bone thickness in the limited resolution regime of in vivo MRI by fuzzy distance transform. IEEE Transactions on Medical Imaging 23:53-62
3. Y. Liu, D. Jin, and P.K. Saha (2013). A new algorithm for trabecular bone thickness computation at low resolution achieved under in vivo condition. Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), 390-393
4. Y. Liu, D. Jin, C. Li, K.F. Janz, T.L. Burns, J.C. Torner, S.M. Levy, P.K. Saha (2014). A robust algorithm for thickness computation at low resolution and its application to in vivo trabecular bone CT imaging. IEEE Transactions on Biomedical Engineering 61:2057-2069

Dr. Saha's research group has developed new cortical bone segmentation algorithms, and a technology has been developed that combines shape mode, post-registration, and warping algorithms to build a mean anatomic space enabling accurate regional comparison of various bone measures in cross-sectional and longitudinal studies.

1. P.K. Saha, G. Liang, J.M. Elkins, A. Coimbra, L.T. Duong, D.S. Williams, and M. Sonka (2011). A new osteophyte segmentation algorithm using partial shape model and its applications to rabbit femur anterior cruciate ligament transection via micro-CT imaging. IEEE Transactions on Biomedical Engineering 58: 2212-2227
2. P.K. Saha and M. Sonka (2012). Apparatus and method for computing regional statistical distribution over a mean anatomic space. US patent #8,189,885
3. C. Li, D. Jin, C. Chen, E.M. Letuchy, K.F. Janz, T.L. Burns, J.C. Torner, S.M. Levy, and P.K. Saha (2015). Automated cortical bone segmentation for multirow detector CT imaging with validation and application to human studies. Med Phy 42 (8):4553-4565
4. P.K. Saha, R. Strand, and G. Borgefors (in press). Digital topology and geometry in medical imaging: a survey. IEEE Transactions on Medical Imaging (invited paper)

Dr. Saha's research group has developed a technique to separate arterial and venous trees in non-contrast pulmonary CT using a novel multi-scale topo-morphologic opening at conjoining locations. Later, this method was applied to segment terminal pulmonary arteries, veins, bronchioles and alveolar duct in high resolution micro-CT imaging for assessment of the morphology of pulmonary acini in mouse lungs.

1. P.K. Saha, Z. Gao, S.K. Alford, M. Sonka, E.A. Hoffman (2010). Topomorphologic separation of fused iso-intensity objects via multi-scale opening: separating arteries and veins in 3-D pulmonary CT. IEEE Transactions on Medical Imaging 29:840-851
2. Z. Gao, R.W. Grout, C. Holtze, E.A. Hoffman, and P.K. Saha (2012). A new paradigm of interactive artery/vein separation in non-contrast pulmonary CT imaging using multi-scale topo-morphologic opening. IEEE Transactions on Biomedical Engineering 59:3016-3027
3. D.M. Vasilescu, Z. Gao, P.K. Saha, L. Yin, G. Wang, B. Haefeli-Bleuer, M. Ochs, E.R. Weibel, E.A. Hoffman (2012). Assessment of morphometry of pulmonary acini in mouse lungs by nondestructive imaging using multi-scale microcomputed tomography. Proceedings of the National Academy of Sciences (PNAS) 109:17105-17110, 2012

• 2014/09/01-2019/08/31
• 1 R01 AR066008, NIH
• Chang(PI)
• MRI of proximal femur microarchitecture as a biomarker of bone quality development, validation, and application of novel methods and algorithms for biomarkers of trabecular bone micro-architecture in human proximal femur bone MR imaging.
• Role: Co-Investigator, PI of sub-contract to University of Iowa

• 2012/08/01-2016/12/31
• 1 R01 HL112986-01A1, NIH
• Hoffman, Eric(PI)
• Multi-center Structural & Functional Quantitative CT Pulmonary Phenotyping
• This proposed bioengineering research partnership seeks to take advantage of the emerging acquisition technique of multi-spectral computed tomography (currently dual energy CT: DECT), careful evaluation of dose lowering methods, and novel approaches to statistical cluster analysis to expand the biomarkers used in multi-center studies to identify sub-populations of lung disease.
• Role: Co-Investigator, PI of the Image Processing Core

• 1998/04/01-2015/06/30
• 3 R01 DE012101-13S1, NIH
• Levy(PI)
• Fluoride and Other Factors in Childhood Bone Development-Supplement
• The goal of this project is to understand how bone develops during childhood/adolescence/early adulthood, including the effects of modifiable and non-modifiable factors. Findings will improve our understanding of the best strategies to optimize skeletal health and prevent future bone disease.
• Role: Co-Investigator; CT based quantitative bone quality assessment.

• 2015/08/01-2020/07/31
• U91 AG108832
• Torner(PI)
• Multicenter Knee Osteoarthritis Study (MOST) Second Renewal: Iowa Clinical Center
• The MOST renewal will focus on new prevention opportunities and also on ways to understand and ultimately limit the impact of knee arthritis on the daily lives of those affected. The goal is to find new strategies to prevent disease at an early stage and to limit the impact of disease once it has occurred.
• Role: Co-Investigator

• 2015/04/15-2020/03/31
• 1R01HL126838, NIH
• Hoffman, Eric(PI)
• Defining the Role of Early Pulmonary Vascular Disease in COPD
• This project evaluates the role of imaging-based measures of pulmonary vascular structure and function to identify smokers at risk of rapid emphysema progression and/or at risk of having frequent acute exacerbations of their COPD.
• Role: Co-Investigator

• 2015/02/17-2016/02/16
• 1S10OD018526, NIH
• Hoffman, Eric(PI)
• Ultra-low Dose, High Speed, High Resolution, Multispectral, Multi-Source MDCT Scanner Equipment grant
• Role: Major User

• 2010/07/24-2015/05/31
• 1 R01 HD062507, NIH
• Shields(PI)
• Mechanical Stress and Skeletal Plasticity after Spinal Cord Injury in Humans
• Role: Co-Investigator; CT based quantitative bone quality assessment

• 2010/06/01-2015/05/30
• 1 RO1 AR056260, NIH
• Regatte(PI)
• Catilage, Bone, and Marrow Interactions in Knee OA
• Role: Co-Investigator, PI of sub-contract to University of Iowa

• 2009/06/18-2013/05/31
• 1 R01 AR054439, NIH
• Saha, Punam(PI)
• Tensor Scale-based Methods for Assessment of Trabecular Bone Quality
• Role: Principal Investigator

• 2010/06/01-2012/05/31
• ICTS/CTSA pilot grant # 1557
• Saha, Punam(PI)
• Treatment effects on quantitative in vivo trabecular bone micro-architectural measures in young adults
• Role: Principal Investigator

• 2006/07/01-2011/06/30
• 1 R01 ARO51376, NIH
• Guo(PI)
• Micro-mechanical Modeling of Trabecular Bone
• Role: Co-Investigator, PI of sub-contract to University of Iowa

• 1999/09/30-2010/07/31
• 5 R01 HL064638
• Hoffman, Eric(PI)
• Image and Model Based Analysis of Lung Diseases
• Role: Co-investigator

• 2005/04/13-2007/02/17
• LKR25567, Merck & Co.
• Saha, Punam(PI)
• Merck/Penn Osteophyte Study Agreement LKR25567
• Role: Principal Investigator

• Iowa Comprehensive Lung Imaging Center (I-CLIC)