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. 23964v1 Announce Type: new Abstract: Self-supervised learning in fluorescence microscopy often relies on 2D projections, despite the inherently three-dimensional nature of cells.
The paper introduces CARNIVAL, a model for protein annotation in cryo-electron tomography (cryo-ET) volumes that leverages simulated data and a forward model to generate domain‑specific augmented paired views for self‑supervised training. By incorporating simulation‑derived protein positions and identities into the architecture and loss function, the model localises semantic information at protein locations. CARNIVAL is evaluated on real tomograms without finetuning and outperforms a state‑of‑the‑art contrastive model that lacks forward‑model paired views or privileged information.
The paper introduces a Geometric-to-Semantic Spherical Transfer Learning framework for labeling cortical sulci on brain surfaces. It first pre‑trains a spherical encoder on ~30,000 unlabeled UK Biobank subjects using only curvature and depth, then injects sulcal fundi lines as a soft‑initialized Topological Prior Injector to bridge the geometric‑semantic gap. Experiments show the method surpasses fully supervised baselines, achieving a mean Dice score of 0.77 and delivering the largest gains on variable and tertiary sulci.
arXiv:2606. 10255v1 Announce Type: cross Abstract: Cryo-electron tomography (cryoET) has emerged as a powerful tool in structural and cellular biology by enabling direct visualization of macromolecular structures within intact cells, thereby linking molecular architecture to cellular organization in a native context.
arXiv:2604.19609v2 Announce Type: replace Abstract: Transformers have become a common foundation across deep learning, yet 3D scene understanding still relies on specialized backbones with strong dom...
arXiv:2606. 00955v1 Announce Type: new Abstract: Despite the growing availability of cryo-electron microscopy (cryo-EM) density maps, effectively leveraging them for protein representation remains challenging.
Pix2Rep-v2 is a self‑supervised learning framework that learns pixel‑ and voxel‑level representations for dense medical imaging tasks, using a redundancy‑reduction objective and equivariance principles to scale to 3D and wide field‑of‑view data. The method is evaluated on four datasets across multiple modalities, tasks, and backbones, demonstrating higher data‑efficiency in few‑shot scenarios and competitive performance, such as a +9.3 Dice point improvement in one‑shot segmentation on the M&Ms‑2 dataset. An in‑context dense prototype approach is also proposed, eliminating the need for downstream training.
arXiv:2609.23019v1 Announce Type: cross Abstract: Soma instance segmentation, i.e., identifying and delineating individual cell somas as distinct instances, is crucial for cellular analysis and conne...
The paper presents a 3D foundation model for light sheet fluorescence microscopy (LSM) that is pretrained on a large curated set of 3D images from various organisms, stains, and imaging protocols. By jointly optimizing for masked reconstruction and image‑text alignment, the model learns transferable volumetric representations that dramatically reduce the need for annotated data. The pretrained backbone enables efficient few‑shot adaptation to downstream tasks such as segmentation, classification, and deblurring, consistently outperforming baselines according to standard metrics and expert evaluation.
arXiv:2606. 03888v1 Announce Type: cross Abstract: Self-supervised learning has enabled large-scale pre-training on 2D natural images, producing general-purpose visual representations that transfer effectively across tasks.
The paper introduces SVRecon, a generalizable neural surface reconstruction framework that uses sparse volumetric representations to achieve high-resolution 3D reconstruction. It employs a two-stage architecture: first predicting occupied voxels with an occupancy network, then rendering only within those regions using specialized sparse algorithms. This approach allows reconstruction at resolutions up to 512³ on 32 GB hardware, producing smoother and more precise surfaces, especially in sparse-view scenarios.
The paper introduces a scalable method to interpret sparse autoencoder (SAE) features in the ESM-2 protein language model by leveraging geometrically inspired features of the protein α‑carbon backbone. Across 8M layers of ESM-2, a false discovery rate–controlled analysis shows that local geometry is significantly associated with many SAE features, revealing substructure within known biological labels and enabling annotation of unannotated metagenomic proteins. Ablation experiments demonstrate that removing these geometric features shifts ESM-2’s predicted contact maps toward the descriptor, linking mechanistic interpretability with structural biology.