Subtomogram Averaging using Dynamo, imod, Relion and MatLab

.MRC and .EM thumbnailer for GNOME

MCP-server for the copick CLI.

Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction.

Automated detection of protein complexes in cryo-electron tomography (cryoET) data. ML models identify five particle classes using a weighted F-β (β=4) metric focused on recall, especially for hard targets, helping reveal cellular “dark matter” and advance biological discovery.

Locating bacterial flagellar motors in cryo-electron tomography slices using YOLOv8l. Fine-tuned on the BYU Kaggle 2025 dataset with mosaic and geometric augmentations, achieving 87.5% mAP50 and 0.52 mAP50-95 on a single T4 GPU.

This project builds machine learning models to automatically detect and classify protein complexes in cryo-electron tomography (cryoET) images, enabling scalable analysis of cellular structures and supporting advanced biological and medical research.

Docker environment for CryoET data analysis

Scaling data analyses in cellular cryoET using comprehensive segmentation.

A napari plugin for copick

A collaborative cryo-ET annotation tool

A Docker-based distribution of Appion-Protomo.

IsoNet at higher resolution

Definitions for a collaborative cryoET annotation tool.

TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.

A curated list of awesome computational cryo-ET methods.

A Modular Platform for Streamlining Automated Cryo-FIB Workflows

Self-supervised learning for isotropic cryoET reconstruction