Microglomeruli Segmentation
Instance segmentation of synaptic boutons in Drosophila brain microscopy, and the tool that ships it to the lab



Fine-tuned MicroSAM (vit_l_lm) on a held-out volume. Each colour is one predicted bouton instance.
A fully reproducible deep-learning pipeline that segments and quantifies synaptic boutons in confocal Z-stacks of the Drosophila mushroom body calyx, plus BoutonViewer: the napari desktop tool that puts the model in the hands of the biologists it was built for. Research and delivery as one project, because a model nobody can run is not a result.
- Fine-tuned MicroSAM (vit_l_lm) with custom post-processing on a hand-annotated 3D dataset built from scratch in napari
- Benchmarked four SOTA 3D instance-segmentation backbones head to head: Cellpose 3D, nnU-Net v2, StarDist 3D and SwinUNETR
- Trained across three preprocessing variants (raw, difference-of-Gaussians, PSF-deconvolved) and evaluated with instance-matching metrics that account for physical voxel volume, not pixel counts
- BoutonViewer reports per-bouton volume and surface area in µm³ / µm², auto-derives voxel calibration from acquisition type, and lets a biologist click away a false positive without touching code
- Final checkpoints published on Hugging Face for reuse