Pinaki Sarder

Pinaki Sarder,

Associate Professor

Department: MD-MED QUANTITATIVE HEALTH
Business Phone: (352) 273-6018
Business Email: pinaki.sarder@ufl.edu

About Pinaki Sarder

Pinaki Sarder is currently an associate professor of AI in the Section of Quantitative Health of the Department of Medicine, as well as the Associate Director for Imaging in the Intelligent Critical Care Center at the University of Florida (UF). Before joining UF, he was an associate professor in the Departments of Pathology & Anatomical Sciences and Biomedical Engineering at the University at Buffalo (UB), where he was at the center of building the computationally enabled graduate program Computational Cell Biology, Anatomy, and Pathology. Prior to UB, he completed post-doctoral training at Mallinckrodt Institute of Radiology at the Washington University in St. Louis (WUSTL) School of Medicine. He received his B.Tech. degree in electrical engineering from the Indian Institute of Technology, Kanpur, in 2003, and M.Sc. and Ph.D. degrees in electrical engineering from WUSTL in 2010.

Dr. Sarder serves on the editorial board of the Journal of the American Society of Nephrology (JASN), is the Associate Editor of IEEE Journal of Biomedical Health Informatics, and a senior member of IEEE. He serves as research co-lead for ASN’s Augmented Intelligence and Digital Health Task Force. He was a recipient of the UB’s Exceptional Scholars – Young Investigator Award in 2018. His research interests include computational fusion of diverse spatial omics data while focusing on diabetic kidney disease. Dr. Sarder’s research is funded by National Institutes of Health, Kidney Precision Medicine Project (KPMP) Consortium, and Human Biomolecular Atlas Project (HubMAP) Consortium.

Additional Positions:
Co-Lead, Unbiased Structural Clustering and Structural Features Work Group
2024 – Current · Kidney Precision Medicine Project Consortium
Member, Research and Scientific Committee
2023 – Current · Renal Pathology Society
Associate Professor (with Tenure) – Department of Health Outcomes and Biomedical Informatics (Affiliate)
2023 – Current · University of Florida
Associate Professor (with Tenure)
2022 – Current · Department of Medicine – Section of Quantitative Health (Primary), Department of Electrical & Computer Engineering and J. Crayton Pruitt Family Department of Biomedical Engineering (Affiliate), University of Florida at Gainesville
Associate Director for Imaging
2022 – Current · Intelligent Critical Care Center, University of Florida
Associate Editor
2022 – Current · Journal of Biomedical and Health Informatics, IEEE
Co-Lead for Research Vision, Augmented Intelligence and Digital Health (AIDH) Task Force
2022 – Current · American Society of Nephrology
Co-Lead, Computational Image Analysis (CIA) Task Force
2022 – Current · Kidney Precision Medicine Project
Member, Various Session Chairs
2020 – Current · SPIE Medical Imaging – Digital & Computational Pathology
Associate Professor (with tenure) – Pathology & Anatomical Sciences and Biomedical Engineering
2021 – 2022 · University at Buffalo
Member, Organizing Committee
2021 – 2021 · AI in Nephropathology Workshop
Assistant Professor – Pathology & Anatomical Sciences and Biomedical Engineering
2015 – 2021 · University at Buffalo
Diversity and Inclusion Advocate, Department of Pathology and Anatomical Sciences
2015 – 2022 · Jacobs School of Medicine & Biomedical Sciences, University at Buffalo
Related Links:

Accomplishments

Senior & Corresponding Author of article selected for the cover of the December 2023 issue of the Kidney 360, "Correlating deep learning-based automated reference kidney histomorphometry with patient demographics and creatinine"
2023 · Kidney 360
Senior & Corresponding Author of the abstract “Automated reference kidney histomorphometry using a panoptic segmentation neural network correlates to patient demographics and creatinine,” which received the honorable mention poster award
2023 · SPIE Digital Pathology 2023
Awarded best abstract and Senior Author of “Automatic segmentation of arteries, arterioles, and glomeruli in renal biopsies with thrombotic microangiopathies,” at the Annual Meeting of the German Society of Nephrology
2021 · Annual Meeting of the German Society of Nephrology
Senior & Corresponding Author of article selected for the cover of the November 2021 issue of the Journal of the American Society of Nephrology, " PodoSighter: A cloud-based tool for label-free podocyte detection in kidney whole slide images,”
2021 · Journal of the American Society of Nephrology
Senior & Corresponding Author of the abstracts: (i) "Prognostic glomerular morphometric phenotype discovery via clustering across large datasets" and (ii) "Urinary proteomics data guides AI to discover new digital biomarkers for diabetic nephropathy classification," which were selected as two out of the three best abstracts for 2020-21
2021 · the Renal Pathology Society
Senior & Corresponding Author of the abstract “Probabilistic modeling of diabetic nephropathy progression,” which was selected as one of the two runner-ups for the Best Poster award
2020-2021 · SPIE Digital Pathology 2020
Senior & Corresponding Author of the article “Computational segmentation and classification of diabetic glomerulosclerosis”
2019 · Best of American Society of Nephrology (ASN) Journals: Clinical Journal of ASN (CJASN) & JASN
Exceptional Scholars – Young Investigator Award
2018 · University at Buffalo
Imaging Sciences Pathway program Graduate Student Fellowship Award
2007 · Washington University in St. Louis

Teaching Profile

Courses Taught
2023-2024
EEL5934 Special Topics in Electrical Engineering
2023
GMS6029 Brain Journal Club
2023-2024
EEL4930 Special Topics in Electrical Engineering

Research Profile

Open Researcher and Contributor ID (ORCID)

0000-0003-2450-5233

Publications

2024
ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2024.03.21.586102. [PMID] 38585837.
2024
Nascent shifts in renal cellular metabolism, structure, and function due to chronic empagliflozin in prediabetic mice.
American journal of physiology. Cell physiology. 326(4):C1272-C1290 [DOI] 10.1152/ajpcell.00446.2023. [PMID] 38602847.
2024
Single-Cell Transcriptional Signatures of Glomerular Disease in Transgenic Mice with APOL1 Variants
Journal of the American Society of Nephrology. [DOI] 10.1681/asn.0000000000000370.
2024
The Banff 2022 Kidney Meeting Work Plan: Data-driven refinement of the Banff Classification for renal allografts
American Journal of Transplantation. 24(3):350-361 [DOI] 10.1016/j.ajt.2023.10.031.
2023
APOL1 kidney risk variants in glomerular diseases modeled in transgenic mice.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2023.03.27.534273. [PMID] 37090576.
2023
Automated Reference Kidney Histomorphometry using a Panoptic Segmentation Neural Network Correlates to Patient Demographics and Creatinine.
Proceedings of SPIE–the International Society for Optical Engineering. 12471 [DOI] 10.1117/12.2655288. [PMID] 37818349.
2023
Banff Digital Pathology Working Group: Image Bank, Artificial Intelligence Algorithm, and Challenge Trial Developments.
Transplant international : official journal of the European Society for Organ Transplantation. 36 [DOI] 10.3389/ti.2023.11783. [PMID] 37908675.
2023
Computational Pathology Fusing Spatial Technologies.
Clinical journal of the American Society of Nephrology : CJASN. 18(5):675-7 [DOI] 10.2215/CJN.0000000000000146. [PMID] 36913267.
2023
Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine
Kidney360. 4(12):1726-1737 [DOI] 10.34067/kid.0000000000000299.
2023
Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2023.05.18.541348. [PMID] 37292965.
2023
Discovery of Novel Digital Biomarkers for Type 2 Diabetic Nephropathy Classification via Integration of Urinary Proteomics and Pathology.
medRxiv : the preprint server for health sciences. [DOI] 10.1101/2023.04.28.23289272. [PMID] 37205413.
2023
Erratum: 89 Bridging Cell Biology and Engineering Sciences: Interdisciplinary Team-based Training in Computational Pathology – ERRATUM.
Journal of clinical and translational science. 7(1) [DOI] 10.1017/cts.2023.553. [PMID] 37396819.
2023
Generative Modeling of Histology Tissue Reduces Human Annotation Effort for Segmentation Model Development.
Proceedings of SPIE–the International Society for Optical Engineering. 12471 [DOI] 10.1117/12.2655282. [PMID] 37818351.
2023
Improving quantification of renal fibrosis using Deep-DUET.
Proceedings of SPIE–the International Society for Optical Engineering. 12471 [DOI] 10.1117/12.2654651. [PMID] 37829619.
2023
NAD metabolism modulates inflammation and mitochondria function in diabetic kidney disease.
The Journal of biological chemistry. 299(8) [DOI] 10.1016/j.jbc.2023.104975. [PMID] 37429506.
2023
Predicting Papillary Renal Cell Carcinoma Prognosis Using Integrative Analysis of Histopathological Images and Genomic Data
Bioinformatics and Biomedical Engineering. 208-221 [DOI] 10.1007/978-3-031-34960-7_15.
2023
Spatially Aware Transformer Networks for Contextual Prediction of Diabetic Nephropathy Progression from Whole Slide Images.
Proceedings of SPIE–the International Society for Optical Engineering. 12471 [DOI] 10.1117/12.2655266. [PMID] 37818350.
2023
Spatially Aware Transformer Networks for Contextual Prediction of Diabetic Nephropathy Progression from Whole Slide Images.
medRxiv : the preprint server for health sciences. [DOI] 10.1101/2023.02.20.23286044. [PMID] 36865174.
2023
Toward Real-World Computational Nephropathology.
Clinical journal of the American Society of Nephrology : CJASN. 18(6):809-812 [DOI] 10.2215/CJN.0000000000000168. [PMID] 37027795.
2022
A cloud-based tool for federated segmentation of whole slide images.
Proceedings of SPIE–the International Society for Optical Engineering. 12039 [DOI] 10.1117/12.2613502. [PMID] 37817879.
2022
A tool for federated training of segmentation models on whole slide images.
Journal of pathology informatics. 13 [DOI] 10.1016/j.jpi.2022.100101. [PMID] 35910077.
2022
A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology
Communications Medicine. 2(1) [DOI] 10.1038/s43856-022-00138-z. [PMID] 35996627.
2022
Automated Tubular Morphometric Visualization for Whole Kidney Biopsy.
Proceedings of SPIE–the International Society for Optical Engineering. 12039 [DOI] 10.1117/12.2613496. [PMID] 37817876.
2022
Computational Integration of Renal Histology and Urinary Proteomics using Neural Networks.
Proceedings of SPIE–the International Society for Optical Engineering. 12039 [DOI] 10.1117/12.2613500. [PMID] 37817878.
2022
Endothelial Cell-Specific Molecule-1 Inhibits Albuminuria in Diabetic Mice.
Kidney360. 3(12):2059-2076 [DOI] 10.34067/KID.0001712022. [PMID] 36591362.
2022
Histo-Fetch – On-the-Fly Processing of Gigapixel Whole Slide Images Simplifies and Speeds Neural Network Training.
Journal of pathology informatics. 13 [DOI] 10.4103/jpi.jpi_59_20. [PMID] 35136674.
2022
HistoLens: A generalizable tool for increasing accessibility and interpretability of quantitative analyses in digital pathology.
Proceedings of SPIE–the International Society for Optical Engineering. 12039 [DOI] 10.1117/12.2613503. [PMID] 37817875.
2022
Integrating image analysis with single cell RNA-seq data to study podocyte-specific changes in diabetic kidney disease.
Proceedings of SPIE–the International Society for Optical Engineering. 12039 [DOI] 10.1117/12.2614495. [PMID] 37817877.
2022
PodoCount: A Robust, Fully Automated, Whole-Slide Podocyte Quantification Tool.
Kidney international reports. 7(6):1377-1392 [DOI] 10.1016/j.ekir.2022.03.004. [PMID] 35694561.
2022
SAM: Self-augmentation mechanism for COVID-19 detection using chest X-ray images
Knowledge-Based Systems. 241 [DOI] 10.1016/j.knosys.2022.108207. [PMID] 35068707.
2022
Variant APOL1 protein in plasma associates with larger particles in humans and mouse models of kidney injury.
PloS one. 17(10) [DOI] 10.1371/journal.pone.0276649. [PMID] 36279295.
2021
A Distributed System Improves Inter-Observer and AI Concordance in Annotating Interstitial Fibrosis and Tubular Atrophy.
Proceedings of SPIE–the International Society for Optical Engineering. 11603 [DOI] 10.1117/12.2581789. [PMID] 34366540.
2021
Automated Computational Detection of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis.
Journal of the American Society of Nephrology : JASN. 32(4):837-850 [DOI] 10.1681/ASN.2020050652. [PMID] 33622976.
2021
Automated detection and quantification of Wilms’ Tumor 1-positive cells in murine diabetic kidney disease.
Proceedings of SPIE–the International Society for Optical Engineering. 11603 [DOI] 10.1117/12.2581387. [PMID] 34366543.
2021
From What to Why, the Growing Need for a Focus Shift Toward Explainability of AI in Digital Pathology.
Frontiers in physiology. 12 [DOI] 10.3389/fphys.2021.821217. [PMID] 35087427.
2021
In Silico Multi-Compartment Detection Based on Multiplex Immunohistochemical Staining in Renal Pathology.
Proceedings of SPIE–the International Society for Optical Engineering. 11603 [DOI] 10.1117/12.2581795. [PMID] 34366541.
2021
PodoSighter: A Cloud-Based Tool for Label-Free Podocyte Detection in Kidney Whole-Slide Images.
Journal of the American Society of Nephrology : JASN. 32(11):2795-2813 [DOI] 10.1681/ASN.2021050630. [PMID] 34479966.
2021
User friendly, cloud based, whole slide image segmentation.
Proceedings of SPIE–the International Society for Optical Engineering. 11603 [DOI] 10.1117/12.2581383. [PMID] 34366542.
2020
Artificial intelligence driven next-generation renal histomorphometry.
Current opinion in nephrology and hypertension. 29(3):265-272 [DOI] 10.1097/MNH.0000000000000598. [PMID] 32205581.
2020
Generative modeling for label-free glomerular modeling and classification.
Proceedings of SPIE–the International Society for Optical Engineering. 11320 [PMID] 32362708.
2020
Generative modeling for renal microanatomy.
Proceedings of SPIE–the International Society for Optical Engineering. 11320 [DOI] 10.1117/12.2549891. [PMID] 32362707.
2020
Improving the accuracy of gastrointestinal neuroendocrine tumor grading with deep learning.
Scientific reports. 10(1) [DOI] 10.1038/s41598-020-67880-z. [PMID] 32632119.
2020
Neutrophil Extracellular Traps (NETs): An unexplored territory in renal pathobiology, a pilot computational study.
Proceedings of SPIE–the International Society for Optical Engineering. 11320 [DOI] 10.1117/12.2549340. [PMID] 32377029.
2020
Probabilistic modeling of Diabetic Nephropathy progression.
Proceedings of SPIE–the International Society for Optical Engineering. 11320 [DOI] 10.1117/12.2549171. [PMID] 32382209.
2020
The Presence and Location of Podocytes in Glomeruli as Affected by Diabetes Mellitus.
Proceedings of SPIE–the International Society for Optical Engineering. 11320 [DOI] 10.1117/12.2548904. [PMID] 32362706.
2019
An integrated iterative annotation technique for easing neural network training in medical image analysis
Nature Machine Intelligence. 1(2):112-119 [DOI] 10.1038/s42256-019-0018-3. [PMID] 31187088.
2019
Computational Segmentation and Classification of Diabetic Glomerulosclerosis.
Journal of the American Society of Nephrology : JASN. 30(10):1953-1967 [DOI] 10.1681/ASN.2018121259. [PMID] 31488606.
2019
Examining Structural Patterns and Causality in Diabetic Nephropathy using inter-Glomerular Distance and Bayesian Graphical Models.
Proceedings of SPIE–the International Society for Optical Engineering. 10956 [DOI] 10.1117/12.2513598. [PMID] 31186597.
2018
Automated erythrocyte detection and classification from whole slide images.
Journal of medical imaging (Bellingham, Wash.). 5(2) [DOI] 10.1117/1.JMI.5.2.027501. [PMID] 29721517.
2018
Cellular Trafficking of Sn-2 Phosphatidylcholine Prodrugs Studied with Fluorescence Lifetime Imaging and Super-resolution Microscopy
Precision Nanomedicine. 1(2):128-145 [DOI] 10.33218/prnano1(2).180724.1. [PMID] 31249994.
2018
Induced Pluripotent Stem Cells Reveal Common Neurodevelopmental Genome Deprograming in Schizophrenia.
Results and problems in cell differentiation. 66:137-162 [DOI] 10.1007/978-3-319-93485-3_6. [PMID] 30209658.
2018
Multi-radial LBP Features as a Tool for Rapid Glomerular Detection and Assessment in Whole Slide Histopathology Images
Scientific Reports. 8(1) [DOI] 10.1038/s41598-018-20453-7. [PMID] 29391542.
2017
Cerebral organoids reveal early cortical maldevelopment in schizophrenia-computational anatomy and genomics, role of FGFR1.
Translational psychiatry. 7(11) [DOI] 10.1038/s41398-017-0054-x. [PMID] 30446636.
2017
Common developmental genome deprogramming in schizophrenia – Role of Integrative Nuclear FGFR1 Signaling (INFS).
Schizophrenia research. 185:17-32 [DOI] 10.1016/j.schres.2016.12.012. [PMID] 28094170.
2017
Computational detection and quantification of human and mouse neutrophil extracellular traps in flow cytometry and confocal microscopy
Scientific Reports. 7(1) [DOI] 10.1038/s41598-017-18099-y. [PMID] 29259241.
2017
Unsupervised labeling of glomerular boundaries using Gabor filters and statistical testing in renal histology.
Journal of medical imaging (Bellingham, Wash.). 4(2) [DOI] 10.1117/1.JMI.4.2.021102. [PMID] 28331889.
2016
Evaluation of Dynamic Optical Projection of Acquired Luminescence for Sentinel Lymph Node Biopsy in Large Animals.
Technology in cancer research & treatment. 15(6):787-795 [PMID] 26376694.
2015
Molecular probes for fluorescence lifetime imaging.
Bioconjugate chemistry. 26(6):963-74 [DOI] 10.1021/acs.bioconjchem.5b00167. [PMID] 25961514.
2015
Protonation and Trapping of a Small pH-Sensitive Near-Infrared Fluorescent Molecule in the Acidic Tumor Environment Delineate Diverse Tumors in Vivo.
Molecular pharmaceutics. 12(12):4237-46 [DOI] 10.1021/acs.molpharmaceut.5b00430. [PMID] 26488921.
2014
Automatic segmentation of fluorescence lifetime microscopy images of cells using multiresolution community detection–a first study.
Journal of microscopy. 253(1):54-64 [DOI] 10.1111/jmi.12097. [PMID] 24251410.
2013
All-near-infrared multiphoton microscopy interrogates intact tissues at deeper imaging depths than conventional single- and two-photon near-infrared excitation microscopes.
Journal of biomedical optics. 18(10) [DOI] 10.1117/1.JBO.18.10.106012. [PMID] 24150231.
2013
Dynamic optical projection of acquired luminescence for aiding oncologic surgery.
Journal of biomedical optics. 18(12) [DOI] 10.1117/1.JBO.18.12.120501. [PMID] 24284472.
2013
Optimization of microfluidic microsphere-trap arrays.
Biomicrofluidics. 7(1) [DOI] 10.1063/1.4793713. [PMID] 24404004.
2013
Performance analysis and design of position-encoded microsphere arrays using the Ziv-Zakai bound.
IEEE transactions on nanobioscience. 12(1):29-40 [DOI] 10.1109/TNB.2012.2230116. [PMID] 23268386.
2012
Fluorescence lifetime imaging microscopy using near-infrared contrast agents.
Journal of microscopy. 247(2):202-7 [DOI] 10.1111/j.1365-2818.2012.03634.x. [PMID] 22788550.
2011
Statistical design of position-encoded microsphere arrays.
IEEE transactions on nanobioscience. 10(1):16-29 [DOI] 10.1109/TNB.2010.2103570. [PMID] 21342857.
2010
Estimating sparse gene regulatory networks using a bayesian linear regression.
IEEE transactions on nanobioscience. 9(2):121-31 [DOI] 10.1109/TNB.2010.2043444. [PMID] 20650703.
2008
Estimating gene signals from noisy microarray images.
IEEE transactions on nanobioscience. 7(2):142-53 [DOI] 10.1109/TNB.2008.2000745. [PMID] 18556262.
2008
Estimating locations of quantum-dot-encoded microparticles from ultra-high density 3-D microarrays.
IEEE transactions on nanobioscience. 7(4):284-97 [DOI] 10.1109/TNB.2008.2011861. [PMID] 19203872.

Grants

Sep 2023 ACTIVE
Computational Image Analysis of Renal Transplant Biopsies to Predict Graft Outcome
Role: Principal Investigator
Funding: NATL INST OF HLTH NIDDK
Jul 2023 ACTIVE
QUantifIEd Coronary Artery Plaque and OuTcomes (QUIET): WARRIOR Ancillary Study
Role: Co-Investigator
Funding: US ARMY MED RES ACQUISITION
Sep 2022 ACTIVE
KPMP Kidney Mapping and Atlas Project (KMAP)
Role: Principal Investigator
Funding: UNIV OF MICHIGAN via NATL INST OF HLTH NIDDK
Sep 2022 ACTIVE
Coordinating and Data Management Center for Acquired Resistance to Therapy Network
Role: Principal Investigator
Funding: ROSWELL PARK COMPREHENSIVE CANCER CTR via NATL INST OF HLTH NCI
Aug 2022 ACTIVE
Computational Image Analysis Platform (CIMAP) for HuBMAP
Role: Principal Investigator
Funding: NATL INST OF HLTH OD
Aug 2022 ACTIVE
A Cloud Based Distributed Tool for Computational Renal Pathology
Role: Principal Investigator
Funding: NATL INST OF HLTH NIDDK
Aug 2022 ACTIVE
Computational Imaging of Renal Structures for Diagnosing Diabetic Nephropathy
Role: Principal Investigator
Funding: NATL INST OF HLTH NIDDK
Aug 2022 – Dec 2023
Rapid quantitative renal fibrosis evaluation with dual-mode microscopy
Role: Principal Investigator
Funding: UNIV OF CALIFORNIA DAVIS via NATL INST OF HLTH NIDDK
Aug 2022 – Jun 2023
Kidney Precision Medicine Project (KPMP): A Computational Renal Pathology Suite for KPMP
Role: Principal Investigator
Funding: WASHINGTON UNIV SAINT LOUIS via NATL INST OF HLTH NIDDK
Jan 2022 ACTIVE
American Cancer Society Institutional Research Grant
Role: Project Manager
Funding: AMERICAN CANCER SOCIETY

Education

Postdoctoral Fellow – Optical Radiology
2011-2015 · Mallinckrodt Institute of Radiology, Washington University School of Medicine in St. Louis
Research Fellow – Biostatistics
2010-2011 · Harvard University School of Public Health
M.Sc., Electrical & Systems Engineering
2010 · Washington University in St. Louis
Ph.D., Electrical & Systems Engineering
2003-2010 · Washington University in St. Louis
B.Tech., Electrical Engineering
1999-2003 · Indian Institute of Technology, Kanpur

Contact Details

Phones:
Business:
(352) 273-6018
Emails:
Addresses:
Business Mailing:
PO Box 100224
GAINESVILLE FL 32610
Business Street:
Division of Intelligent Critical Care Center
PO Box 100224
GAINESVILLE FL 32611