arXiv subjects

Pinaki Sarder

Publications and source records attributed to Pinaki Sarder.

12 recordsLinked to original sources

arXiv2026

Evaluating Usability in Biomedical Visualization: Rethinking Heuristic Evaluation for Spatial Omics and Multidisciplinary Research Platforms

Introduction: Clinical research informatics (CRI) platforms support biomedical discovery by integrating advanced computational tools into research workflows. Emerging technologies such as spatial omics and AI-enabled imaging expand research capabilities but introduce complex interfaces that increase cognitive burden and alter established analytical processes. Traditional usability frameworks identify general usability issues but often miss challenges specific to high-dimensional biomedical data. Methods: We conducted two complementary studies involving 39 participants to evaluate conventional usability heuristics and identify CRI-specific criteria. Study 1 included 19 undergraduates completing interactive tasks, and Study 2 involved 20 clinical professionals completing an asynchronous hierarchical task framework. Observational and interview data were analyzed using deductive coding based on standard usability heuristics and emerging CRI-specific themes. Results: Simultaneous presentation of complex data overlays and analytical tools overwhelmed users, particularly those with limited spatial-omics experience. Participants relied on trial-and-error exploration and struggled with unlabeled tools in data-rich environments. Feedback indicated that users benefit from phased onboarding, contextual guidance, and progressive feature introduction rather than immediate access to all functionality. Discussion: High-dimensional research platforms require domain-specific usability criteria beyond traditional frameworks. We propose three specialized heuristics: Active Parameter Transparency, Point-of-Use Guidance, and Phased Feature Disclosure. These heuristics help developers manage complexity, provide contextual support, and improve accessibility for multidisciplinary research teams.

cs.HC↗

arXiv2026

A Comprehensive Benchmark of Histopathology Foundation Models for Kidney Digital Pathology Images

Histopathology foundation models (HFMs), pretrained on large-scale cancer datasets, have advanced computational pathology. However, their applicability to non-cancerous chronic kidney disease remains underexplored, despite coexistence of renal pathology with malignancies such as renal cell and urothelial carcinoma. We systematically evaluate 11 publicly available HFMs across 11 kidney-specific downstream tasks spanning multiple stains (PAS, H&E, PASM, and IHC), spatial scales (tile and slide-level), task types (classification, regression, and copy detection), and clinical objectives, including detection, diagnosis, and prognosis. Tile-level performance is assessed using repeated stratified group cross-validation, while slide-level tasks are evaluated using repeated nested stratified cross-validation. Statistical significance is examined using Friedman test followed by pairwise Wilcoxon signed-rank testing with Holm-Bonferroni correction and compact letter display visualization. To promote reproducibility, we release an open-source Python package, kidney-hfm-eval, available at https://pypi.org/project/kidney-hfm-eval/ , that reproduces the evaluation pipelines. Results show moderate to strong performance on tasks driven by coarse meso-scale renal morphology, including diagnostic classification and detection of prominent structural alterations. In contrast, performance consistently declines for tasks requiring fine-grained microstructural discrimination, complex biological phenotypes, or slide-level prognostic inference, largely independent of stain type. Overall, current HFMs appear to encode predominantly static meso-scale representations and may have limited capacity to capture subtle renal pathology or prognosis-related signals. Our results highlight the need for kidney-specific, multi-stain, and multimodal foundation models to support clinically reliable decision-making in nephrology.

cs.CV↗

arXiv2025

Interactive visualization of kidney micro-compartmental segmentations and associated pathomics on whole slide images

Application of machine learning techniques enables segmentation of functional tissue units in histology whole-slide images (WSIs). We built a pipeline to apply previously validated segmentation models of kidney structures and extract quantitative features from these structures. Such quantitative analysis also requires qualitative inspection of results for quality control, exploration, and communication. We extend the Vitessce web-based visualization tool to enable visualization of segmentations of multiple types of functional tissue units, such as, glomeruli, tubules, arteries/arterioles in the kidney. Moreover, we propose a standard representation for files containing multiple segmentation bitmasks, which we define polymorphically, such that existing formats including OME-TIFF, OME-NGFF, AnnData, MuData, and SpatialData can be used. We demonstrate that these methods enable researchers and the broader public to interactively explore datasets containing multiple segmented entities and associated features, including for exploration of renal morphometry of biopsies from the Kidney Precision Medicine Project (KPMP) and the Human Biomolecular Atlas Program (HuBMAP).

q-bio.QM↗

arXiv2025

PathDiff: Histopathology Image Synthesis with Unpaired Text and Mask Conditions

Diffusion-based generative models have shown promise in synthesizing histopathology images to address data scarcity caused by privacy constraints. Diagnostic text reports provide high-level semantic descriptions, and masks offer fine-grained spatial structures essential for representing distinct morphological regions. However, public datasets lack paired text and mask data for the same histopathological images, limiting their joint use in image generation. This constraint restricts the ability to fully exploit the benefits of combining both modalities for enhanced control over semantics and spatial details. To overcome this, we propose PathDiff, a diffusion framework that effectively learns from unpaired mask-text data by integrating both modalities into a unified conditioning space. PathDiff allows precise control over structural and contextual features, generating high-quality, semantically accurate images. PathDiff also improves image fidelity, text-image alignment, and faithfulness, enhancing data augmentation for downstream tasks like nuclei segmentation and classification. Extensive experiments demonstrate its superiority over existing methods.

cs.CV↗

arXiv2025

CASC-AI: Consensus-aware Self-corrective Learning for Noise Cell Segmentation

Multi-class cell segmentation in high-resolution gigapixel whole slide images (WSIs) is crucial for various clinical applications. However, training such models typically requires labor-intensive, pixel-wise annotations by domain experts. Recent efforts have democratized this process by involving lay annotators without medical expertise. However, conventional non-corrective approaches struggle to handle annotation noise adaptively because they lack mechanisms to mitigate false positives (FP) and false negatives (FN) at both the image-feature and pixel levels. In this paper, we propose a consensus-aware self-corrective AI agent that leverages the Consensus Matrix to guide its learning process. The Consensus Matrix defines regions where both the AI and annotators agree on cell and non-cell annotations, which are prioritized with stronger supervision. Conversely, areas of disagreement are adaptively weighted based on their feature similarity to high-confidence consensus regions, with more similar regions receiving greater attention. Additionally, contrastive learning is employed to separate features of noisy regions from those of reliable consensus regions by maximizing their dissimilarity. This paradigm enables the model to iteratively refine noisy labels, enhancing its robustness. Validated on one real-world lay-annotated cell dataset and two reasoning-guided simulated noisy datasets, our method demonstrates improved segmentation performance, effectively correcting FP and FN errors and showcasing its potential for training robust models on noisy datasets. The official implementation and cell annotations are publicly available at https://github.com/ddrrnn123/CASC-AI.

cs.CV↗

arXiv2021

Histo-fetch -- On-the-fly processing of gigapixel whole slide images simplifies and speeds neural network training

We created a custom pipeline (histo-fetch) to efficiently extract random patches and labels from pathology whole slide images (WSIs) for input to a neural network on-the-fly. We prefetch these patches as needed during network training, avoiding the need for WSI preparation such as chopping/tiling. We demonstrate the utility of this pipeline to perform artificial stain transfer and image generation using the popular networks CycleGAN and ProGAN, respectively.

eess.IV↗

arXiv2021

A tool for user friendly, cloud based, whole slide image segmentation

Convolutional neural networks, the state of the art for image segmentation, have been successfully applied to histology images by many computational researchers. However, the translatability of this technology to clinicians and biological researchers is limited due to the complex and undeveloped user interface of the code, as well as the extensive computer setup required. As an extension of our previous work (arXiv:1812.07509), we have developed a tool for segmentation of whole slide images (WSIs) with an easy to use graphical user interface. Our tool runs a state-of-the-art convolutional neural network for segmentation of WSIs in the cloud. Our plugin is built on the open source tool HistomicsTK by Kitware Inc. (Clifton Park, NY), which provides remote data management and viewing abilities for WSI datasets. The ability to access this tool over the internet will facilitate widespread use by computational non-experts. Users can easily upload slides to a server where our plugin is installed and perform human in the loop segmentation analysis remotely. This tool is open source, and has the ability to be adapted to segment of any pathological structure. For a proof of concept, we have trained it to segment glomeruli from renal tissue images, achieving an F-score > 0.97 on holdout tissue slides.

eess.IV↗

arXiv2020

Neural Network Segmentation of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis in Renal Biopsies

Glomerulosclerosis, interstitial fibrosis, and tubular atrophy (IFTA) are histologic indicators of irrecoverable kidney injury. In standard clinical practice, the renal pathologist visually assesses, under the microscope, the percentage of sclerotic glomeruli and the percentage of renal cortical involvement by IFTA. Estimation of IFTA is a subjective process due to a varied spectrum and definition of morphological manifestations. Modern artificial intelligence and computer vision algorithms have the ability to reduce inter-observer variability through rigorous quantitation. In this work, we apply convolutional neural networks for the segmentation of glomerulosclerosis and IFTA in periodic acid-Schiff stained renal biopsies. The convolutional network approach achieves high performance in intra-institutional holdout data, and achieves moderate performance in inter-intuitional holdout data, which the network had never seen in training. The convolutional approach demonstrated interesting properties, such as learning to predict regions better than the provided ground truth as well as developing its own conceptualization of segmental sclerosis. Subsequent estimations of IFTA and glomerulosclerosis percentages showed high correlation with ground truth.

q-bio.TO↗

arXiv2020

Unsupervised Community Detection with a Potts Model Hamiltonian, an Efficient Algorithmic Solution, and Applications in Digital Pathology

Unsupervised segmentation of large images using a Potts model Hamiltonian is unique in that segmentation is governed by a resolution parameter which scales the sensitivity to small clusters. Here, the input image is first modeled as a graph, which is then segmented by minimizing a Hamiltonian cost function defined on the graph and the respective segments. However, there exists no closed form solution of this optimization, and using previous iterative algorithmic solution techniques, the problem scales quadratically in the Input Length. Therefore, while Potts model segmentation gives accurate segmentation, it is grossly underutilized as an unsupervised learning technique. We propose a fast statistical down-sampling of input image pixels based on the respective color features, and a new iterative method to minimize the Potts model energy considering pixel to segment relationship. This method is generalizable and can be extended for image pixel texture features as well as spatial features. We demonstrate that this new method is highly efficient, and outperforms existing methods for Potts model based image segmentation. We demonstrate the application of our method in medical microscopy image segmentation; particularly, in segmenting renal glomerular micro-environment in renal pathology. Our method is not limited to image segmentation, and can be extended to any image/data segmentation/clustering task for arbitrary datasets with discrete features.

cs.CV↗

arXiv2018

Iterative annotation to ease neural network training: Specialized machine learning in medical image analysis

Neural networks promise to bring robust, quantitative analysis to medical fields, but adoption is limited by the technicalities of training these networks. To address this translation gap between medical researchers and neural networks in the field of pathology, we have created an intuitive interface which utilizes the commonly used whole slide image (WSI) viewer, Aperio ImageScope (Leica Biosystems Imaging, Inc.), for the annotation and display of neural network predictions on WSIs. Leveraging this, we propose the use of a human-in-the-loop strategy to reduce the burden of WSI annotation. We track network performance improvements as a function of iteration and quantify the use of this pipeline for the segmentation of renal histologic findings on WSIs. More specifically, we present network performance when applied to segmentation of renal micro compartments, and demonstrate multi-class segmentation in human and mouse renal tissue slides. Finally, to show the adaptability of this technique to other medical imaging fields, we demonstrate its ability to iteratively segment human prostate glands from radiology imaging data.

eess.IV↗

arXiv2017

Multi-radial LBP Features as a Tool for Rapid Glomerular Detection and Assessment in Whole Slide Histopathology Images

We demonstrate a simple and effective automated method for the segmentation of glomeruli from large (~1 gigapixel) histopathological whole-slide images (WSIs) of thin renal tissue sections and biopsies, using an adaptation of the well-known local binary patterns (LBP) image feature vector to train a support vector machine (SVM) model. Our method offers high precision (>90%) and reasonable recall (>70%) for glomeruli from WSIs, is readily adaptable to glomeruli from multiple species, including mouse, rat, and human, and is robust to diverse slide staining methods. Using 5 Intel(R) Core(TM) i7-4790 CPUs with 40 GB RAM, our method typically requires ~15 sec for training and ~2 min to extract glomeruli reproducibly from a WSI. Deploying a deep convolutional neural network trained for glomerular recognition in tandem with the SVM suffices to reduce false positives to below 3%. We also apply our LBP-based descriptor to successfully detect pathologic changes in a mouse model of diabetic nephropathy. We envision potential clinical and laboratory applications for this approach in the study and diagnosis of glomerular disease, and as a means of greatly accelerating the construction of feature sets to fuel deep learning studies into tissue structure and pathology.

q-bio.TO↗

arXiv2013

Automatic Segmentation of Fluorescence Lifetime Microscopy Images of Cells Using Multi-Resolution Community Detection

We have developed an automatic method for segmenting fluorescence lifetime (FLT) imaging microscopy (FLIM) images of cells inspired by a multi-resolution community detection (MCD) based network segmentation method. The image processing problem is framed as identifying segments with respective average FLTs against a background in FLIM images. The proposed method segments a FLIM image for a given resolution of the network composed using image pixels as the nodes and similarity between the pixels as the edges. In the resulting segmentation, low network resolution leads to larger segments and high network resolution leads to smaller segments. Further, the mean-square error (MSE) in estimating the FLT segments in a FLIM image using the proposed method was found to be consistently decreasing with increasing resolution of the corresponding network. The proposed MCD method outperformed a popular spectral clustering based method in performing FLIM image segmentation. The spectral segmentation method introduced noisy segments in its output at high resolution. It was unable to offer a consistent decrease in MSE with increasing resolution.

physics.med-ph↗