Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
This is an accompanying repository to the work doi:10.1101/2024.12.28.630444 and the dataset of 1829 cryo-electron tomograms presented within. This repository serves as a central location for exchnage of additional resources and community contributions related to this dataset. The intended audience includes researchers and practitioners in cryo-electron tomography, structural biology, and visual proteomics. It is designed for those interested in exploring large-scale cryo-ET datasets, developing new analysis tools, or contributing annotations and resources to advance the field. Students and educators in related disciplines may also find the repository valuable for learning and teaching. Licensing information can be found in LICENSE.
The tomograms are available for download from EMPIAR-11830 and CZI-10302. Parameters of data acquisition are listed in Section Cryo-ET data acquisition of the article.
Available sets:
- Tilt-series in
EERformat & Metadata (26.8TB) - Reconstructions (bin4) denoised with cryo-CARE (3.6TB) - These files are not 3D CTF-corrected
- Reconstructions (bin4) 3D CTF-corrected with IMOD (1.8TB) - These files are not cryo-CARE denoised
We welcome contributions from the community to enhance the utility of this dataset. Read how you can get involved in CONTRIBUTING.md. We look forward to seeing your contributions!
Particle annotations of ATPase, Microtubule, Nucleosome, Clathrin, Photosystem II, Rubisco, Ribosome
Article: Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Authors: Kelley, R., Khavnekar, S., Righetto, R.D., Heebner, J., Obr, M., Zhang, X., Chakraborty, S., Tagiltsev, G., Michael, A.K., van Dorst, S., Waltz, F., McCafferty, C.L., Lamm, L., Zufferey, S., Van der Stappen, P., van den Hoek, H., Wietrzynski, W., Harar, P., Wan, W., Briggs, J.A.G., Plitzko, J.M., Engel, B.D., Kotecha, A.
DOI: 10.1101/2024.12.28.630444
REPO: github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Subfolder in this repository: 10.1101-2024.12.28.630444
Data source & version: EMPIAR (as of 28.02.2025)
Article: Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Authors: Kelley, R., Khavnekar, S., Righetto, R.D., Heebner, J., Obr, M., Zhang, X., Chakraborty, S., Tagiltsev, G., Michael, A.K., van Dorst, S., Waltz, F., McCafferty, C.L., Lamm, L., Zufferey, S., Van der Stappen, P., van den Hoek, H., Wietrzynski, W., Harar, P., Wan, W., Briggs, J.A.G., Plitzko, J.M., Engel, B.D., Kotecha, A.
DOI: 10.1101/2024.12.28.630444
REPO: github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Subfolder in this repository: 10.5281-zenodo.13941456/
Paper: Scaling data analyses in cellular cryoET using comprehensive segmentation
Authors: Last, M.G.F., Voortman, L.M. and Sharp, T.H.
DOI: 10.1101/2025.01.16.633326
REPO: github.com/bionanopatterning/Pom
APP: https://cryopom.streamlit.app
Segmented features: cytoplasm, mitochondrion, nuclear envelope, nucleoplasm, pyrenoid tube, thylakoid, vesicle, Golgi, pyrenoid, stroma, lipid droplet, endoplasmic reticulum, nuclear pore complex, starch granule, cilum, intermediate-filament rich areas, cell wall, chloroplast outer membrane, dense layer, membrane, ribosome, ATP synthase, RuBisCo, TRiC, proteasome.
Subfolder in this repository: 10.1101-2025.01.16.633326
Data source & version: CryoET Data Portal deposition 10314
Authors: Righetto, R.D. & Van der Stappen, P.
REPO: github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Subfolder in this repository: chlamydataset2relion5
Authors: Van der Stappen, P. & Waltz, F.
DOI: 10.5281/zenodo.15358525
REPO: github.com/TomoGuide/TomoGuide.github.io
Subfolder in this repository: 10.5281-zenodo.15358525