arXiv Computer Vision
Sep 21

Catena: A Comprehensive Software Suite for Large-Scale Connectomics

Catena is an open‑source, developer‑centric software suite designed to streamline large‑scale connectomics from electron microscopy data. It integrates modules for 3D neuron and organelle segmentation, synapse detection, microtubule tracking, and neurotransmitter inference into composable, chunk‑wise pipelines that are fully documented and extensible. The suite includes pretrained machine learning models, containerized runtimes, and shareable components to reduce compute and ground‑truth data needs while ensuring reproducible, scalable processing across workstations and clusters.

By Samia Mohinta, Pedro G\'omez-G\'alvez, Shi Yan Lee, Daniel Franco-Barranco, Michael Clayton, Stephan Preibisch, Jan Funke, Albert Cardona
arXiv AI
5d ago

Atelier: Learning Local Self-Supervised Features for CryoEM Volumes via Hypernetworks

Atelier is a self‑supervised framework that uses a transformer‑based hypernetwork to generate implicit neural representations (INRs) for cryo‑EM maps, enabling efficient, scale‑agnostic, coordinate‑conditioned feature extraction. Trained on 5,439 maps from the Electron Microscopy Data Bank, the pretrained INR provides continuous local feature fields that can be used as auxiliary channels for a 3D nested U‑Net, improving voxel‑level property prediction across eight tasks compared to a volume‑only baseline. The approach demonstrates that amortized INRs can serve as a geometry‑aware primitive for large‑scale cryo‑EM analysis.

By Phillip Lo, Sudarshan Babu, Dari Kimanius, Aly A. Khan