Deconvolution methods for 3-D fluorescence microscopy images. - Pinaki Sarder; Arye Nehorai (IEEE Signal Process. Mag., 2006)

Gene Reachability Using Page Ranking on Gene Co-expression Networks. - Pinaki Sarder; Weixiong Zhang; J. Perren Cobb; Arye Nehorai (Link Mining, 2010)

Statistical design of position-encoded microsphere arrays at low target concentrations. - Xiaoxiao Xu; Pinaki Sarder; Arye Nehorai (ACSCC, 2011)

Segmenting Intracellular Distribution Images Derived by Fluorescent Dyes Using a Potts Model Hamiltonian - Dandan Hu; Pinaki Sarder; Peter Ronhovde; Sharon Bloch; Samuel Achilefu; Zohar Nussinov (CoRR, 2012)

Automated renal histopathology: digital extraction and quantification of renal pathology. - Pinaki Sarder; Brandon Ginley; John Tomaszewski 001 (Digital Pathology, 2016)

Identification and characterization of neutrophil extracellular trap shapes in flow cytometry. - Brandon Ginley; Tiffany Emmons; Prabhu Sasankan; Constantin Urban; Brahm H. Segal; Pinaki Sarder (Digital Pathology, 2017)

Automatic computational labeling of glomerular textural boundaries. - Brandon Ginley; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2017)

Leveraging unsupervised training sets for multi-scale compartmentalization in renal pathology. - Brendon Lutnick; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2017)

Computational analysis of the structural progression of human glomeruli in diabetic nephropathy. - Brandon G. Ginley; John Tomaszewski 001; Kuang-Yu Jen; Agnes B. Fogo; Sanjay Jain 006; Pinaki Sarder (Digital Pathology, 2018)

Glomerular detection and segmentation from multimodal microscopy images using a Butterworth band-pass filter. - Darshana Govind; Brandon Ginley; Brendon Lutnick; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2018)

Deep variational auto-encoders for unsupervised glomerular classification. - Brendon Lutnick; Rabi Yacoub; Kuang-Yu Jen; John Tomaszewski 001; Sanjay Jain 006; Pinaki Sarder (Digital Pathology, 2018)

Examining structural changes in diabetic nephropathy using inter-nuclear distances in glomeruli: a comparison of variously automated methods. - Olivier Simon; Rabi Yacoub; Sanjay Jain 006; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2018)

Iterative annotation to ease neural network training: Specialized machine learning in medical image analysis. - Brendon Lutnick; Brandon Ginley; Darshana Govind; Sean D. McGarry; Peter S. LaViolette; Rabi Yacoub; Sanjay Jain 006; John Tomaszewski 001; Kuang-Yu Jen; Pinaki Sarder (CoRR, 2018)

Computational analysis of cerebrovascular structures imaged using two-photon microscopy. - Siddhartha Dhiman; Itender Singh; Pinaki Sarder (Digital Pathology, 2019)

Examining structural patterns and causality in diabetic nephropathy using inter-glomerular distance and Bayesian graphical models. - Aurijoy Majumdar; Kuang-Yu Jen; Sanjay Jain 006; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2019)

An integrated iterative annotation technique for easing neural network training in medical image analysis. - Brendon Lutnick; Brandon Ginley; Darshana Govind; Sean D. McGarry; Peter S. LaViolette; Rabi Yacoub; Sanjay Jain 006; John Tomaszewski 001; Kuang-Yu Jen; Pinaki Sarder (Nat. Mach. Intell., 2019)

Probabilistic modelling of diabetic nephropathy progression. - Samuel P. Border; Kuang-Yu Jen; Washington L. C. dos-Santos; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2020)

Fully automated classification of glomerular lesions in lupus nephritis. - Brandon Ginley; Kuang-Yu Jen; Avi Rosenberg; Giovanni Maria Rossi; Sanjay Jain 006; Pinaki Sarder (Digital Pathology, 2020)

Deep learning-based automated hot-spot detection and tumor grading in human gastrointestinal neuroendocrine tumor. - Darshana Govind; Kuang-Yu Jen; Pinaki Sarder (Digital Pathology, 2020)

Generative modeling for label-free glomerular modeling and classification. - Brendon Lutnick; Brandon Ginley; Kuang-Yu Jen; Wen Dong 001; Pinaki Sarder (Digital Pathology, 2020)

The presence and location of podocytes in glomeruli as affected by diabetes mellitus. - Kathryn E. Maraszek; Briana A. Santo; Rabi Yacoub; John Tomaszewski 001; Imtiaz Mohammad; Amber M. Worral; Pinaki Sarder (Digital Pathology, 2020)

Generative modeling for renal microanatomy. - Leema Krishna Murali; Brendon Lutnick; Brandon Ginley; John Tomaszewski 001; Pinaki Sarder (Digital Pathology, 2020)

Neutrophil Extracellular Traps (NETs): an unexplored territory in renal pathobiology, a pilot computational study. - Briana A. Santo; Brahm H. Segal; John Tomaszewski 001; Imtiaz Mohammad; Amber M. Worral; Sanjay Jain 006; Michelle B. Visser; Pinaki Sarder (Digital Pathology, 2020)

Unsupervised Community Detection with a Potts Model Hamiltonian, an Efficient Algorithmic Solution, and Applications in Digital Pathology. - Brendon Lutnick; Wen Dong 001; Zohar Nussinov; Pinaki Sarder (CoRR, 2020)

Neural Network Segmentation of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis in Renal Biopsies. - Brandon Ginley; Kuang-Yu Jen; Avi Rosenberg; Felicia Yen; Sanjay Jain 006; Agnes B. Fogo; Pinaki Sarder (CoRR, 2020)

Automated detection and quantification of Wilms' Tumor 1-positive cells in murine diabetic kidney disease. - Darshana Govind; Briana A. Santo; Brandon Ginley; Rabi Yacoub; Avi Z. Rosenberg; Kuang-Yu Jen; Vighnesh Walavalkar; Gregory E. Wilding; Amber M. Worral; Imtiaz Mohammad; Pinaki Sarder (Digital Pathology, 2021)

In silico multi-compartment detection based on multiplex immunohistochemical staining in renal pathology. - Kuang-Yu Jen; Leema Krishna Murali; Brendon Lutnick; Brandon Ginley; Darshana Govind; Hidetoshi Mori; Guofeng Gao; Pinaki Sarder (Digital Pathology, 2021)

User friendly, cloud based, whole slide image segmentation. - Brendon Lutnick; Avinash Kammardi Shashiprakash; David Manthey; Pinaki Sarder (Digital Pathology, 2021)

A distributed system improves inter-observer and AI concordance in annotating interstitial fibrosis and tubular atrophy. - Avinash Kammardi Shashiprakash; Brendon Lutnick; Brandon Ginley; Darshana Govind; Nicholas J. Lucarelli; Kuang-Yu Jen; Avi Z. Rosenberg; Anatoly Urisman; Vighnesh Walavalkar; Jonathan E. Zuckerman; Marco Delsante; Mei Lin Z. Bissonnette; et al. (Digital Pathology, 2021)

Histo-fetch - On-the-fly processing of gigapixel whole slide images simplifies and speeds neural network training. - Brendon Lutnick; Leema Krishna Murali; Brandon Ginley; Pinaki Sarder (CoRR, 2021)

Predicting the Visual Attention of Pathologists Evaluating Whole Slide Images of Cancer. - Souradeep Chakraborty; Rajarsi Gupta 001; Ke Ma 005; Darshana Govind; Pinaki Sarder; Won-Tak Choi; Waqas Mahmud; Eric Yee; Felicia Allard; Beatrice Knudsen; Gregory J. Zelinsky; Joel H. Saltz; et al. (MOVI@MICCAI, 2022)

HistoLens: a generalizable tool for increasing accessibility and interpretability of quantitative analyses in digital pathology. - Samuel P. Border; Brandon Ginley; John E. Tomaszewski; Pinaki Sarder (Digital and Computational Pathology, 2022)

Integrating image analysis with single cell RNA-seq data to study podocyte-specific changes in diabetic kidney disease. - Darshana Govind; Saber Meamardoost; Rabi Yacoub; Rudiyanto Gunawan; John E. Tomaszewski; Pinaki Sarder (Digital and Computational Pathology, 2022)

Automated tubular morphometric visualization for whole kidney biopsy. - Neil Kavthekar; Brandon Ginley; Samuel P. Border; Nicholas J. Lucarelli; Kuang-Yu Jen; Pinaki Sarder (Digital and Computational Pathology, 2022)

Computational integration of renal histology and urinary proteomics using neural networks. - Nicholas J. Lucarelli; Donghwan Yun; Dohyun Han; Brandon Ginley; Kyung Chul Moon; Avi Rosenberg; John Tomaszewski 001; Seung Seok Han; Pinaki Sarder (Digital and Computational Pathology, 2022)

A cloud-based tool for federated segmentation of whole slide images. - Brendon Lutnick; David Manthey; Jan U. Becker; Jonathan E. Zuckerman; Luis Rodrigues; Kuang Yu Jen; Pinaki Sarder (Digital and Computational Pathology, 2022)

SAM: Self-augmentation mechanism for COVID-19 detection using chest X-ray images. - Usman Muhammad; Md. Ziaul Hoque; Mourad Oussalah 002; Anja Keskinarkaus; Tapio Seppänen; Pinaki Sarder (Knowl. Based Syst., 2022)

Predicting Papillary Renal Cell Carcinoma Prognosis Using Integrative Analysis of Histopathological Images and Genomic Data. - Shaira Limson Kee; Michael Aaron G. Sy; Samuel P. Border; Nicholas J. Lucarelli; Akshita Gupta; Pinaki Sarder; Marvin C. Masalunga; Myles Joshua Toledo Tan (IWBBIO (2), 2023)

Improving quantification of renal fibrosis using deep-DUET. - Samuel P. Border; Avi Rosenberg; Jarcy Zee; Richard M. Levenson 001; Kuang-Yu Jen; Pinaki Sarder; Farzad Fereidouni (Digital and Computational Pathology, 2023)

Automated reference kidney histomorphometry using a panoptic segmentation neural network correlates to patient demographics and creatinine. - Brandon Ginley; Nicholas J. Lucarelli; Jarcy Zee; Sanjay Jain 006; Seung Seok Han; Luis Rodrigues; Michelle L. Wong; Kuang-Yu Jen; Pinaki Sarder (Digital and Computational Pathology, 2023)

Generative modeling of histology tissue reduces human annotation effort for segmentation model development. - Brendon Lutnick; Nicholas J. Lucarelli; Pinaki Sarder (Digital and Computational Pathology, 2023)

Spatially aware transformer networks for contextual prediction of diabetic nephropathy progression from whole slide images. - Benjamin Shickel; Nicholas J. Lucarelli; Adish Rao; Donghwan Yun; Kyung Chul Moon; Seung Seok Han; Pinaki Sarder (Digital and Computational Pathology, 2023)

The Triple Aim of a Semester-Long Course in Science, Technology, and Society. - Myles Joshua Toledo Tan; Alfredo Bayu Satriya; Shaira Limson Kee; Michael Aaron G. Sy; Pinaki Sarder (TALE, 2023)

CASC-AI: Consensus-aware Self-corrective AI Agents for Noise Cell Segmentation. - Ruining Deng; Yihe Yang; David J. Pisapia; Benjamin Liechty; Junchao Zhu; Juming Xiong; Junlin Guo; Zhengyi Lu; Jiacheng Wang; Xing Yao; Runxuan Yu; Rendong Zhang; et al. (CoRR, 2025)

PathDiff: Histopathology Image Synthesis with Unpaired Text and Mask Conditions. - Mahesh Bhosale; Abdul Wasi; Yuanhao Zhai 001; Yunjie Tian; Samuel P. Border; Nan Xi; Pinaki Sarder; Junsong Yuan 001; David S. Doermann; Xuan Gong (CoRR, 2025)