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.

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.