- On Kaggle
- On CryoET Data Portal
This repository contains notebooks to facilitate entries in the CZ CryoET ML Challenge. These notebooks are organized as follows:
- overview.ipynb: how to use, visualize, process, and sample the cryoET datasets
- blob_detector_inference.ipynb: a fast end-to-end example of processing zarrs and generating a submission
- 3d_unet_monai: training and inference notebooks using a 3D UNet with MONAI and PyTorch
- DeepFindET: training and inference using a Tensorflow-based 3D UNet
- tomotwin_picking_notebook: training and inference with the TomoTwin cryo-ET embedding model
- copick documentation
- MONAI documentation
- TomoTwin documentation
- copick GitHub repository
- copick-utils GitHub repository
- copick-torch GitHub repository
- DeepFindET GitHub repository
This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to [email protected].
If you believe you have found a security issue, please responsibly disclose by contacting us at [email protected].