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.
By Bogdan Toader, Kiarash Jamali, Tanmay A. M. Bharat, Sjors H. W. Scheres
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.
By Dan Luo, Xuan Lin, Peng Zhou, Junwen Zhu, Tengfei Ma, Xiangxiang Zeng, Yiping Liu
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
arXiv:2604.10766v5 Announce Type: replace
Abstract: Open-set 3D macromolecule detection in cryogenic electron tomography eliminates the need for target-specific model retraining. However, strict VRAM...
By Ming-Yang Ho, Alberto Bartesaghi
arXiv:2610.01358v1 Announce Type: cross
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a widely adopted technique for biomolecular structure determination. The conventional c...
By Advaith Maddipatla, M\"art-Erik M\"aeots, Marco Pegoraro, Nikolaus Dr\"ager, Roberto Covino, Sanketh Vedula, Martin Pacesa, Alex M. Bronstein
arXiv:2606. 31332v1 Announce Type: new Abstract: Protein automodeling from cryo-EM density maps faces unique challenges in enforcing physicochemical validity and managing conformational heterogeneity.
By Minzhang Li, Mingrui Li, Weichen Qin, Qihe Chen, Sixian Shen, Yuan Pei, Jiakai Zhang, Jingyi Yu
arXiv:2609.36429v1 Announce Type: new
Abstract: Predicting gene expression from H&E-stained histology images offers a scalable alternative to costly spatial transcriptomics, yet most existing methods...
By Zijun Gao, Chunbin Gu, Jinxi Xiang, Xiangde Luo, Pheng-Ann Heng
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:2609.14097v1 Announce Type: cross
Abstract: Subtomogram classification in cryo-electron tomography (cryo-ET) is a challenging problem due to the scarcity of labeled examples. While cryo-ET simu...
By Siddhant Bharadwaj, Ashish Vashist, Rashi Singh, Pranav Vinodh, Nishanth Artham, Runmin Jiang, Xingjian Li, Min Xu
arXiv:2609.13665v1 Announce Type: new
Abstract: Accurate cell segmentation remains a major bottleneck in subcellular spatial transcriptomics (SST), in which morphological images and spatially resolve...
By Xinyu Shu, Andrew Zhang, Jean Yang, Jinman Kim
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...
By Mohammad Khateri, Morteza Ghahremani, Jussi Tohka, Alejandra Sierra
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.
By Arash Fatehi, Robin Ebbestad, Linus Butt, Hans Blom, Sigrid Lundberg, Hannes Olauson, Hjalmar Brismar, David Unnersj\"o-Jess, Thomas Benzing, Katarzyna Bozek