Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Ron Kelley, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, Grigory Tagiltsev, Alicia K. Michael, Sofie van Dorst, Florent Waltz, Caitlyn L. McCafferty, Lorenz Lamm, Simon Zufferey, Philippe Van der Stappen, Hugo van den Hoek, Wojciech Wietrzynski, Pavol Harar, William Wan, John A.G. Briggs, Jürgen M. Plitzko, Benjamin D. Engel, Abhay Kotecha
This is an accompanying repository to the work (doi:10.1016/j.molcel.2025.11.029 & preprint 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 exchange 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 (now published in: doi:10.1016/j.molcel.2025.11.029)
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.
Zenodo DOI: 10.5281/zenodo.15615650 (Note: doi changed due to version change)
REPO: github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Subfolder in this repository: 10.5281-zenodo.15615650
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.
Zenodo DOI: 10.5281/zenodo.15875786
REPO: github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Subfolder in this repository: 10.5281-zenodo.15875786
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.
Zenodo DOI: 10.5281/zenodo.16619468
REPO: github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Subfolder in this repository: 10.5281-zenodo.16619468
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.
Zenodo DOI: 10.5281/zenodo.15358525
REPO: github.com/TomoGuide/TomoGuide.github.io
Subfolder in this repository: 10.5281-zenodo.15358525
Article: In-cell architecture of the mitochondrial respiratory chain
Authors: Waltz, F., Righetto, R.D., Lamm, L., Salinas-Giegé, T., Kelley, R., Zhang, X., Obr, M., Khavnekar, S., Kotecha, A., Engel, B.D.
DOI: 10.1126/science.ads8738
REPO: github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Subfolder in this repository: 10.1126-science.ads8738
Data source & version: EMPIAR (as of 28.02.2025)
Author: Ricardo D. Righetto
REPO: github.com/Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Subfolder in this repository: chlamy2025