arXiv:2608.30768v1 Announce Type: new Abstract: Automatic neuron reconstruction from light microscopy images is a central problem in computational neuroanatomy. While recent methods have achieved enc...
Automatic neuron reconstruction from light microscopy images is a central problem in computational neuroanatomy. While recent methods have achieved encouraging results on local image blocks, it remain...
arXiv:2608. 09636v1 Announce Type: cross Abstract: Accurate 3D neuron segmentation in fluorescence microscopy is critical for neuroscience.
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.
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.
arXiv:2606. 14975v1 Announce Type: cross Abstract: How the wiring and functional organization of cortex shape recurrent computation remains a central question in both neuroscience and machine learning.
The paper introduces a 3D residual wavelet diffusion model for super‑resolving ultra low‑field MRI scans. By using a lossless wavelet reparameterisation, residual shifting, and domain randomisation, the method fits whole‑brain data on a single GPU, speeds up sampling, and generalises across scanners. It achieves volumetric accuracy comparable to leading regression approaches while producing per‑voxel uncertainty maps that reveal under‑determined regions and preserves disease‑relevant atrophy in cognitively impaired subjects.
arXiv:2609.10456v1 Announce Type: new Abstract: Nanoscale imaging of mammalian brains is critical for connectomics. X-ray laminography enables high-throughput imaging of extended, plate-like biologic...
arXiv:2608. 07575v1 Announce Type: cross Abstract: Confocal microscopy of optically cleared and swelled tissue resolves complex biological structures in 3D, but such acquisitions are highly anisotropic: along the under-sampled axial direction the structure can appear discontinuous, hampering reconstruction and automated quantitative analysis.
arXiv:2609.31204v1 Announce Type: cross Abstract: Recent fMRI foundation models differ substantially in the spatial scale at which they represent brain activity. ROI- and connectivity-based models ar...
arXiv:2607. 17782v1 Announce Type: cross Abstract: Foundation models pretrained using self-supervised learning have transformed computer vision by learning transferable representations from large-scale unlabeled data.
The paper introduces a transfer‑learning framework that pre‑trains an implicit neural representation (INR) on a high‑resolution diffusion MRI template and then adapts it to individual subjects through registration and fine‑tuning. This approach enables native single‑subject super‑resolution, achieving a 4× through‑plane up‑sampling from 5 mm to 1.25 mm on Human Connectome Project data. Compared to a recent baseline, the method reduces NRMSE by 36–49 % and increases FSIM by 24–43 %, while training 6× faster and outperforming other INR‑based techniques on both image quality and domain‑specific metrics.