CryoVirusDB: An Expert Labelled Cryo-EM Image Dataset for AI-Driven Virus Particle recognition and Extraction
CryoVirusDB is a dataset of labeled virus particles in cryo-EM micrographs (images) for training and testing machine learning methods of virus particle picking. This repository contains scripts used to crawl, download, process, annotate, and post procress the CryoVirusDB dataset.
Figure: Conceptual overview of Cryo-EM single particle analysis from particle selection to 3D reconstruction of virus. (A) Stack of ideal micrographs where the true virus particles are picked (encircled yellow), (B) Extracted virus particles from micrographs with fixed box size. (C) Multiple 2D classes to facilitate stack cleaning and the removal of false particles. (D) Reconstructed 3D structure of the virus from 2D images using series of computational techniques.
Path to CryoVirusDB Dataset: https://calla.rnet.missouri.edu/CryoVirusDB/
Each EMPIAR ID in CryoVirusDB is available as a compressed file (tar.gz) that can be downloaded by simply clicking on the file. Once you have downloaded the file, you must extract its contents. If you are using a Windows operating system, you can use tools such as WinRAR or 7zip to extract the file.
OR
To download and extract dataset (ex: 11060), use command:
wget https://calla.rnet.missouri.edu/CryoVirusDB/11060.tar.gz
tar -zxvf 11060.tar.gz -C
Option 2: Use scripts to download all the cryo-EM micrographs from EMPIAR and virus particles coordinates from Zenodo
git clone https://github.com/BioinfoMachineLearning/CryoVirusDB.git
cd download_micrographs
python download_micrographs_from_EMPIAR.py
These commands will enable you to download all the motion corrected micrographs from EMPIAR. Next, you should retrieve the virus particle labels from Zenodo by accessing this link: https://zenodo.org/record/10397742
If storage space is a concern, researchers can opt for a more lightweight version of CryoVirusDB called CryoVirusDB_Lite.
CryoVirusDB_Lite includes truncated versions of the original micrographs and particle ground truth files that result in a total storage size of 76 GB, making it easier to store and transfer. This version includes an 8-bit representation of micrographs in JPG format, along with the necessary particle coordinate files for 9 Cryo-EM virus datasets.
Path to CryoVirusDB_Lite Dataset: https://calla.rnet.missouri.edu/CryoVirusDB_Lite/
The steps to download and extract the data files are identical to the instructions provided in option 1.
CryoVirusDB is an expert-labeled dataset containing coordinates of accurately selected virus particles in cryo-EM micrographs. CryoVirusDB comprises 9,941 micrographs featuring 9 different viruses along with the coordinates of 0.3 Million virus particles in total. We anticipate that CryoVirusDB will enhance the capabilities of deep learning in accurately identifying virus particles in cryo-EM micrographs, thereby facilitating the subsequent 2D-3D reconstruction process.
Each data folder (titled after the corresponding EMPIAR dataset ID) for all expert labelled data includes the following: motion corrected micrographs, ground truth, and particles stack.
Statistics of true virus particles for each EMPIAR database in CryoVirusDB:
| SN | EMPAIR ID | Virus Type | Number of Micrographs |
Micrograph size | Particle Diameter (px) |
Number of True Virus Particles |
|---|---|---|---|---|---|---|
| 1 | 10192 | Feline calicivirus | 1000 | (4096, 4096) | 470 | 9660 |
| 2 | 11060 | Nudaurelia capensis omega virus | 1276 | (4096, 4096) | 516 | 11916 |
| 3 | 10203 | Macrobrachium rosenbergii nodavirus | 1000 | (3838, 3710) | 377 | 16601 |
| 4 | 10033 | Human parechovirus 3 | 1000 | (4096, 4096) | 350 | 55732 |
| 5 | 10652 | Coxsackievirus | 1127 | (3838, 3710) | 374 | 11144 |
| 6 | 10341 | Bovine enterovirus | 1274 | (4096, 4096) | 376 | 22694 |
| 7 | 10193 | Feline calicivirus | 1000 | (4096, 4096) | 516 | 96126 |
| 8 | 10205 | Cowpea mosaic virus | 1000 | (4096, 4096) | 310 | 81037 |
| 9 | 10555 | Nudaurelia capensis omega virus | 1264 | (4096, 4096) | 564 | 34488 |
| Total | 9941 | 339398 |
Researchers can use CryoVirusDB to train and test their Machine Learning / Deep Learning based methods for automated cryo-EM virus particle picking.
Users are supposed to use motion corrected 2D images (micrographs) as input. The virus particle's coordinate information for corresponding micrographs are located inside 'ground_truth' >> 'particle_coordinates' folder. The file naming convention for both the micrographs and their corresponding particle's coordinate are same for user's ease.
For EMPIAR 11060, the motion corrected micrograph is: 11060>>micrographs>>micrograph1.mrc and the corresponding particle's coordinate information is found here: 11060>>ground_truth>>particle_coordinates>>micrograph1.csv
The particle stack is: 11060>>particles_stack>>micrograph1.mrc and the corresponding star file for all virus particles in EMPIAR 11060 is store as .star file in: 11060>>ground_truth>>empiar-micrograph1.star
Open Access
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** Link to CryoVirusDB paper ** : https://www.biorxiv.org/content/10.1101/2023.12.25.573312v1
If you use the code or data associated with this research work or otherwise find this data useful, please cite: \
@article {Gyawali2023.12.25.573312,
author = {Rajan Gyawali and Ashwin Dhakal and Liguo Wang and Jianlin Cheng},
title = {CryoVirusDB: A Labeled Cryo-EM Image Dataset for AI-Driven Virus Particle Picking},
year = {2023},
doi = {10.1101/2023.12.25.573312},
publisher = {Cold Spring Harbor Laboratory},
journal = {bioRxiv}
URL = { https://www.biorxiv.org/content/10.1101/2023.12.25.573312v1 }
}