arXiv subjects

Suyog Jadhav

Publications and source records attributed to Suyog Jadhav.

3 recordsLinked to original sources

arXiv2026

SAM for Robust Mitochondria Instance Segmentation in Fluorescence Microscopy

The morphological analysis of mitochondria in fluorescence microscopy (FM) is crucial for understanding cellular health, energy production, and metabolic regulation. While foundation models like the Segment Anything Model (SAM) have revolutionized natural image segmentation, their direct application to FM is hindered by a significant domain shift characterized by diffraction-limited resolution, low contrast, and complex overlapping organelle networks. Furthermore, the development of robust models is bottlenecked by a severe lack of high-quality, manually annotated instance segmentation datasets for mitochondria. In this paper, we propose a scalable solution to this data scarcity by finetuning SAM exclusively on synthetically generated FM data. We simulate realistic mitochondria data and emulate the optical properties of fluorescence microscopes to create a large-scale annotated dataset. We evaluate our fine-tuned model on a curated dataset of real, manually annotated FM images. Qualitative and quantitative analyses demonstrate that our synthetically fine-tuned model improves precision and average dice score over strong baselines. This work establishes the potential of simulation-assisted training for FM instance segmentation.

cs.CV↗

arXiv2020

Artefact removal in ground truth and noise model deficient sub-cellular nanoscopy images using auto-encoder deep learning

Image denoising or artefact removal using deep learning is possible in the availability of supervised training dataset acquired in real experiments or synthesized using known noise models. Neither of the conditions can be fulfilled for nanoscopy (super-resolution optical microscopy) images that are generated from microscopy videos through statistical analysis techniques. Due to several physical constraints, supervised dataset cannot be measured. Due to non-linear spatio-temporal mixing of data and valuable statistics of fluctuations from fluorescent molecules which compete with noise statistics, noise or artefact models in nanoscopy images cannot be explicitly learnt. Therefore, such problem poses unprecedented challenges to deep learning. Here, we propose a robust and versatile simulation-supervised training approach of deep learning auto-encoder architectures for the highly challenging nanoscopy images of sub-cellular structures inside biological samples. We show the proof of concept for one nanoscopy method and investigate the scope of generalizability across structures, noise models, and nanoscopy algorithms not included during simulation-supervised training. We also investigate a variety of loss functions and learning models and discuss the limitation of existing performance metrics for nanoscopy images. We generate valuable insights for this highly challenging and unsolved problem in nanoscopy, and set the foundation for application of deep learning problems in nanoscopy for life sciences.

eess.IV↗

arXiv2020

Multi-Plateau Ensemble for Endoscopic Artefact Segmentation and Detection

Endoscopic artefact detection challenge consists of 1) Artefact detection, 2) Semantic segmentation, and 3) Out-of-sample generalisation. For Semantic segmentation task, we propose a multi-plateau ensemble of FPN (Feature Pyramid Network) with EfficientNet as feature extractor/encoder. For Object detection task, we used a three model ensemble of RetinaNet with Resnet50 Backbone and FasterRCNN (FPN + DC5) with Resnext101 Backbone}. A PyTorch implementation to our approach to the problem is available at https://github.com/ubamba98/EAD2020.

cs.CV↗