OpenCell Microscopy Images
Version v1.0, source
released 08 Dec 2021
source
released 08 Dec 2021- Leonetti Lab (Chan Zuckerberg Biohub San Francisco)
- Mann Lab (Max Plank Institute)
The OpenCell microscopy images were taken alongside immunoprecipitation-mass spectrometry data to investigate protein localization and protein-protein interactions in the same cellular context. It contains confocal fluorescent microscopy images of live HEK293T cells. Each image has one protein endogenously tagged with GFP and DNA stained with Hoechst 33342. Across the dataset, 1,310 proteins were tagged, with each protein represented by four to six field-of-view images with z-stacks in 16-bit TIFF files.
Dataset Overview
Data Type
Fluorescence microscopy images
Citation
Publication: OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (2022). https://doi.org/10.1126/science.abi6983
Dataset: OpenCell on AWS was accessed on [DATE] from https://registry.opendata.aws/czb-opencell.
Dataset Card Authors
Chan Zuckerberg Initiative
Dataset Card Contact
virtualcellmodels@chanzuckerberg.comUses
Primary Use Cases
Investigate cellular localization of proteins in live, single cells
Out-of-Scope or Unauthorized Use Cases
Do not use the dataset for the following purposes:
- Usage not covered by the license.
- Any use that is not in accordance with the Acceptable Use Policy
Dataset Structure
Each folder contains images for one tagged protein and there are four to six field-of-view images, each with a z-stack of around 100 slices per channel. A maximum-intensity z-projection is also provided. There are two channels for each image, the first one is for DNA and the second one is for the GFP-tagged protein.
Personal and Sensitive Information
No personal and sensitive information is included.
Dataset Creation
Curation Rationale
These images were taken alongside immunoprecipitation-mass spectrometry data to study protein localization and protein-protein interactions in the same cellular context
Data Collection and Processing
Cells were imaged live with Hoechst stain using a confocal microscope driven by automated image acquisition. The raw z-stack TIFF images and a maximum-projection of the z-stack are provided. More details see https://www.science.org/doi/10.1126/science.abi6983
Annotation process
The localization of each protein is annotated manually using three “grades”: grade 3 indicates a very prominent localization, grade 2 indicates unambiguous but less prominent localization, and grade 1 indicates weak or barely detectable localization. To obtain the annotations and see more details: https://opencell.czbiohub.org/download.
Who are the annotators?
The annotation was done by the team who generated and processed the data.
Bias, Risks, and Limitations
- GFP tags sometimes could impact protein localization and protein-protein interactions.
- Proteins may behave differently in different cell lines and cell types.
Acknowledgements
See source reference: https://www.science.org/doi/10.1126/science.abi6983