Anwesha Sarkar

Rayna Andreeva, Anwesha Sarkar, Rik Sarkar

The tongue surface houses a range of papillae that are integral to the mechanics and chemistry of taste and textural sensation. Although gustatory function of papillae is well investigated, the uniqueness of papillae within and across individuals remains elusive. Here, we present the first machine learning framework on 3D microscopic scans of human papillae (n = 2092), uncovering the uniqueness of geometric and topological features of papillae. The finer differences in shapes of papillae are investigated computationally based on a number of features derived from discrete differential geometry and computational topology. Interpretable machine learning techniques show that persistent homology features of the papillae shape are the most effective in predicting the biological variables. Models trained on these features with small volumes of data samples predict the type of papillae with an accuracy of 85%. The papillae type classification models can map the spatial arrangement of filiform and fungiform papillae on a surface. Remarkably, the papillae are found to be distinctive across individuals and an individual can be identified with an accuracy of 48% among the 15 participants from a single papillae. Collectively, this is the first unprecedented evidence demonstrating that tongue papillae can serve as a unique identifier inspiring new research direction for food preferences and oral diagnostics.

Jaydeep Rade, Soumik Sarkar, Anwesha Sarkar et al.

Recent developments in deep learning-based methods demonstrated its potential to predict the 3D protein structures using inputs such as protein sequences, Cryo-Electron microscopy (Cryo-EM) images of proteins, etc. However, these methods struggle to predict the protein complexes (PC), structures with more than one protein. In this work, we explore the atomic force microscope (AFM) assisted deep learning-based methods to predict the 3D structure of PCs. The images produced by AFM capture the protein structure in different and random orientations. These multi-view images can help train the neural network to predict the 3D structure of protein complexes. However, obtaining the dataset of actual AFM images is time-consuming and not a pragmatic task. We propose a virtual AFM imaging pipeline that takes a 'PDB' protein file and generates multi-view 2D virtual AFM images using volume rendering techniques. With this, we created a dataset of around 8K proteins. We train a neural network for 3D reconstruction called Pix2Vox++ using the synthesized multi-view 2D AFM images dataset. We compare the predicted structure obtained using a different number of views and get the intersection over union (IoU) value of 0.92 on the training dataset and 0.52 on the validation dataset. We believe this approach will lead to better prediction of the structure of protein complexes.

Shreyan Ganguly, Angona Biswas, Jaydeep Rade et al.

Foundation vision-language models (VLMs) excel on natural images, but their utility for biomedical microscopy remains underexplored. In this paper, we investigate how in-context learning enables state-of-the-art VLMs to perform few-shot object detection when large annotated datasets are unavailable, as is often the case with microscopic images. We introduce the Micro-OD benchmark, a curated collection of 252 images specifically curated for in-context learning, with bounding-box annotations spanning 11 cell types across four sources, including two in-lab expert-annotated sets. We systematically evaluate eight VLMs under few-shot conditions and compare variants with and without implicit test-time reasoning tokens. We further implement a hybrid Few-Shot Object Detection (FSOD) pipeline that combines a detection head with a VLM-based few-shot classifier, which enhances the few-shot performance of recent VLMs on our benchmark. Across datasets, we observe that zero-shot performance is weak due to the domain gap; however, few-shot support consistently improves detection, with marginal gains achieved after six shots. We observe that models with reasoning tokens are more effective for end-to-end localization, whereas simpler variants are more suitable for classifying pre-localized crops. Our results highlight in-context adaptation as a practical path for microscopy, and our benchmark provides a reproducible testbed for advancing open-vocabulary detection in biomedical imaging.

Juntao Zhang, Angona Biswas, Jaydeep Rade et al.

Atomic Force Microscopy (AFM) enables high-resolution surface imaging at the nanoscale, yet the output is often degraded by artifacts introduced by environmental noise, scanning imperfections, and tip-sample interactions. To address this challenge, a lightweight and fully automated framework for artifact detection and restoration in AFM image analysis is presented. The pipeline begins with a classification model that determines whether an AFM image contains artifacts. If necessary, a lightweight semantic segmentation network, custom-designed and trained on AFM data, is applied to generate precise artifact masks. These masks are adaptively expanded based on their structural orientation and then inpainted using a directional neighbor-based interpolation strategy to preserve 3D surface continuity. A localized Gaussian smoothing operation is then applied for seamless restoration. The system is integrated into a user-friendly GUI that supports real-time parameter adjustments and batch processing. Experimental results demonstrate the effective artifact removal while preserving nanoscale structural details, providing a robust, geometry-aware solution for high-fidelity AFM data interpretation.