Pinaki Sarder PhD
Pinaki Sarder
PhD
Assistant Professor
Department of Pathology and Anatomical Sciences
Jacobs School of Medicine & Biomedical Sciences
Specialty/Research Focus
Bioinformatics; Biomedical Image Analysis; Biomedical Imaging; Digital Pathology; Image Analysis; Machine Learning; Quantitative Histology
Professional Summary:
We develop novel computational methods to study and understand tissue micro-anatomy using multi-modal whole-slide microscopy images as well as associated genomic datasets. Our method facilitates decision making in a clinical work-flow (both for diagnosis and predicting progression of diseases), and also allows studying fundamental systems biology of disease dynamics. Currently, our major focus involves studying diabetic kidney diseases in mouse models and human samples.
Education and Training:
- Postdoctoral Fellow, Optical Radiology, Washington University in St. Louis, School of Medicine (2015)
- Fellowship, Biostatistics, Harvard University, School of Public Health (2011)
- MS, Electrical Engineering, Washington University in St. Louis (2010)
- PhD, Electrical Engineering, Washington University in St. Louis (2010)
- BS, Electrical Engineering, Indian Institute of Technology, Kanpur (2003)
Employment:
- Assistant Professor, Pathology and Anatomical Sciences, University at Buffalo, The State University of New York (2015-present)
Awards and Honors:
- Recipient, University at Buffalo Exceptional Scholars - Young Investigator Award (2018)
- Marshal, School of Engineering and Applied Science, Washington University in St. Louis, Commencement (2010)
- Recipient, Imaging Sciences Pathway program Graduate Student Fellowship, Washington University School of Medicine (2007)
Research Expertise:
- Digital Pathology
- Image Analysis
- Image Processing
Research Centers:
- Center of Excellence in Bioinformatics and Life Sciences
- Center for Computational Research (CCR)
Grants and Sponsored Research:
- September 2018–July 2023
R01: Computational Imaging of Renal Structures for Diagnosing Diabetic Nephropathy
National Institutes of Health
Role: Principal Investigator
$1,485,400 - April 2019–March 2020
Computational Analysis of Neutrophil Extracellular Traps in Lupus Nephritis Renal Biopsies
CKD Biomarkers Consortium Pilot and Feasibility Program
Role: Principal Investigator
$75,000 - November 2017–October 2019
Computational Imaging of Renal Structures for Diagnosing Diabetic Nephropathy
DiaComp Pilot & Feasibility Grant
Role: Principal Investigator
$100,000
Journal Articles:
- Lutnick B, Ginley B, Govind D, McGarry SD, LaViolette PS, Yacoub R, Jain S, Tomaszewski JE, Jen KY, Sarder P. An Integrated Iterative Annotation Technique for Easing Neural Network Training in Medical Image Analysis. Nat Mach Intell. 2019; 1(2).
- Majumdar A, Jen KY, Jain S, Tomaszewski JE, Sarder P. Examining Structural Patterns and Causality in Diabetic Nephropathy using inter-Glomerular Distance and Bayesian Graphical Models. Proc SPIE Int Soc Opt Eng. 2019; 10956.
- Maji D, Lu J, Sarder P, Schmieder AH, Cui G, Yang X, Pan D, Lew MD, Achilefu S, Lanza GM. Cellular Trafficking of Sn-2 Phosphatidylcholine Prodrugs Studied with Fluorescence Lifetime Imaging and Super-resolution Microscopy. Precis Nanomed. 2018; 1(2).
- Govind D, Lutnick B, Tomaszewski JE, Sarder P. Automated erythrocyte detection and classification from whole slide images. J Med Imaging (Bellingham). 2018; 5(2).
- Simon O, Yacoub R, Jain S, Tomaszewski JE, Sarder P. Multi-radial LBP Features as a Tool for Rapid Glomerular Detection and Assessment in Whole Slide Histopathology Images. Sci Rep. 2018; 8(1).
- Narla ST, Decker B, Sarder P, Stachowiak EK, Stachowiak MK. Induced Pluripotent Stem Cells Reveal Common Neurodevelopmental Genome Deprograming in Schizophrenia. Results Probl Cell Differ. 2018; 66.
- Ginley BG, Emmons T, Lutnick B, Urban CF, Segal BH, Sarder P. Computational detection and quantification of human and mouse neutrophil extracellular traps in flow cytometry and confocal microscopy. Sci Rep. 2017; 7(1).
- Narla ST, Lee YW, Benson CA, Sarder P, Brennand KJ, Stachowiak EK, Stachowiak MK. Common developmental genome deprogramming in schizophrenia - Role of Integrative Nuclear FGFR1 Signaling (INFS). Schizophr Res. 2017; 185.
- Ginley, B, Tomaszewski JE, Yacoub R, Chen F, Sarder P. Unsupervised Labeling of Glomerular Boundaries Using Gabor Filters and Statisical Testing in Renal Histology. epub. 2017.
- Lutnick, B, Tomaszewski JE, Sarder P. Leveraging Unsupervised Training Sets for Multi-Scale Compartmentization in Renal Pathology. Proc SPIE Medical Imaging. 2017.
- Ginley, B, Tomaszewski JE, Sarder P. Automatic computational labeling of glomerular textural boundaries.. Digital Pathology. 2017.
- Sarder P, Ginley B, Tomaszewski J. Automated renal histopathology: Digital extraction and quantification of renal pathology. Proc SPIE. 2016; 9791.
- Sarder P, Grinley, B, Tomaszewski JE. Automated renal histopathology: Digital extraction and quantification of renal pathology.. SPIE. 2016.
- Gilson RC, Tang R, Som A, Klajer C, Sarder P, Sudlow GP, Akers WJ, Achilefu S. Protonation and Trapping of a Small pH-Sensitive Near-Infrared Fluorescent Molecule in the Acidic Tumor Environment Delineate Diverse Tumors in Vivo. Mol Pharm. 2015; 12(12).
- Ringhausen E, Wang T, Pitts J, Sarder P, Akers WJ. Evaluation of Dynamic Optical Projection of Acquired Luminescence for Sentinel Lymph Node Biopsy in Large Animals. Technol Cancer Res Treat. 2015.
- Sarder P, Maji D, Achilefu S. Molecular Probes for Fluorescence Lifetime Imaging. Bioconjug Chem. 2015; 26(6).
- Hu D*, Sarder P*, Ronhovde P, Achilefu S, Nussinov Z. Community detection for fluorescent lifetime microscopy image segmentation. Proc SPIE. 2014; 8949.
- Sarder P, Akers W, Sudlow G, Yazdanfar S, Achilefu S. Quantitative determination of maximal imaging depth in all-NIR multiphoton microscopy images of thick tissues. Proc SPIE. 2014; 8948.
- Xu X, Li Z, Sarder P, Kotagori N, Nehorai A. Simultaneous detection of multiple biological targets using optimized microfluidic microsphere-trap arrays. J Micro/Nanolith MEMS MOEMS. 2014; 13(1).
- Hu D*, Sarder P*, Ronhovde P, Orthaus S, Achilefu S, Nussinov Z. Automatic segmentation of fluorescence lifetime microscopy images of cells using multiresolution community detection--a first study. J Microsc. 2014; 253(1).
- Sarder P, Gullicksrud K, Mondal S, Sudlow GP, Achilefu S, Akers WJ. Dynamic optical projection of acquired luminescence for aiding oncologic surgery. J Biomed Opt. 2013; 18(12).
- Sarder P, Yazdanfar S, Akers WJ, Tang R, Sudlow GP, Egbulefu C, Achilefu S. All-near-infrared multiphoton microscopy interrogates intact tissues at deeper imaging depths than conventional single- and two-photon near-infrared excitation microscopes. J Biomed Opt. 2013; 18(10).
- Xu X, Sarder P, Kotagiri N, Achilefu S, Nehorai A. Performance analysis and design of position-encoded microsphere arrays using the Ziv-Zakai bound. IEEE Trans Nanobioscience. 2013; 12(1).
- Xu X*, Sarder P*, Li Z*, Nehorai A. Optimization of microfluidic microsphere-trap arrays. Biomicrofluidics. 2013; 7(1).
- Nothdurft R*, Sarder P*, Bloch S, Culver J, Achilefu S. Fluorescence lifetime imaging microscopy using near-infrared contrast agents. J Microsc. 2012; 247(2).
- Sarder P, Nehorai A. Statistical design of position-encoded microsphere arrays. IEEE Trans Nanobioscience. 2011; 10(1).
- Sarder P, Schierding W, Cobb JP, Nehorai A. Estimating sparse gene regulatory networks using a bayesian linear regression. IEEE Trans Nanobioscience. 2010; 9(2).
- Sarder P, Nehorai A. Estimating locations of quantum-dot-encoded microparticles from ultra-high density 3-D microarrays. IEEE Trans Nanobioscience. 2008; 7(4).
- Sarder P, Nehorai A, Davis PH, Stanley SL. Estimating gene signals from noisy microarray images. IEEE Trans Nanobioscience. 2008; 7(2).
- Sarder P, Nehorai A. Deconvolution methods for 3D fluorescence microscopy images: An overview. IEEE Signal Process Mag. 2006; 23(3).
Books and Book Chapters:
- Sarder P, Zhang W, Cobb JP, Nehorai A. Gene reachability using Page ranking on gene co-expression networks. Link Mining: Models, Algorithms, and Applications. 2010.
Presentations:
- "AI for Biomedical & Clinical Applications: A Key for the Next Generation Renaissance Scientists" Department of Pathology and Anatomical Sciences, University at Buffalo (2019)
- "Introduction to digital pathology using examples from renal pathology" Department of Physics, Washington University in St. Louis (2018)
- "Automated quantification of glomeruli features in renal pathology" SPIE Medical Imaging, SPIE, Digital Pathology (2016)
Service Activities:
- Session: Computational Image Analysis: Shaping the Future of Nephropathology, The American Society of Nephrology's The Kidney Week 2019; Moderator (2019)
- Program Chair, 32nd Conference on Graphics, Patterns, and Images, SIBGRAPI 2019; Chair (2019)
- Program Committee, 2019 IEEE International Workshop on Machine Learning for Signal Processing; Member (2019)
- Plos One; Associate Editor (2018–2021)
- Faculty Diversity and Inclusion Committee, School of Medicine & Biomedical Sciences, University at Buffalo; Department Representative (2015–present)