Imaging data

Published Data

General useful data sources

Imaging data at the EMBL-EBI:

BioImage Archive - stores and distributes biological images that are useful to life-science researchers currently in development. In its first phase, the BioImage Archive will provide archiving services to EMPIAR. Image data currently in BioStudies will also be migrated to the BioImage Archive, whilst new direct image-data submissions will be accepted by BioStudies, Cell-IDR or Tissue-IDR.
Electron Microscopy Public Image Archive(EMPIAR) - public resource for raw electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure.

Data available from research groups in Sweden

The list of available data on this Portal was curated manually until February 2022. After February 2022, we instead began to use a script to query the Europe PMC database (making use of their API) in order to locate relevant publications. We only include data from publications about COVID-19/SARS-CoV-2 that BOTH involve at least one author affiliated with a Swedish research institution AND openly share reusable data and/or code. The code used for the query is written in Python and, as with all of our code, it is openly available in GitHub. We welcome others to reuse it and to repurpose it for other pathogens.

The lists of available data may not be exhaustive as the script used to generate it does not search for every possible database/repository. If you find that a dataset is missing, or that the information related to it is incorrect, please get in touch with us

Last updated: 2024-03-04

Data types

All data types (273)

Biochemistry data (34)

Drug discovery data (15)

Genomics & transcriptomics data (82)

Health data (98)

Imaging data (7)

Other data (45)

Protein data (43)

Public health data (65)

Serology data (21)

Social science and humanities data (62)

Publication	Available dataset and code
Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry Sengar A., Cervantes M., Bondalapati S. T., Hess T., et al (2023) American Society for Microbiology DOI: 10.1128/jvi.01992-22	Movies and data to accompany the study data zenodo: 7826331 Image and time series analysis code written in MATLAB is available on GitHub code GitHub
Nanoscale binding site localization by molecular distance estimation on native cell surfaces using topological image averaging Kumra Ahnlide V., Kumra Ahnlide J., Wrighton S., Beech J. P., et al (2022) eLife Sciences Publications, Ltd DOI: 10.7554/elife.64709	SiteLocalization software for binding site localisation on non-homogeneous cell surfaces using topological image averaging code GitHub FluoroDist.jl - software for simulated fluorescence images with accurate surface distances code GitHub Site localisation measurements data data Dryad
Presence of hyaluronan in lung alveoli in severe Covid-19: An opening for new treatment options? Hellman U., Karlsson M. G., Engström-Laurent A., Cajander S., et al (2021) Elsevier BV DOI: 10.1074/jbc.AC120.015967	Color light micrographs of autopsy lung tissue from the three Covid-19 cases, all included in the article. data
Infection of Brain Pericytes Underlying Neuropathology of COVID-19 Patients Bocci M., Oudenaarden C., Sàenz-Sardà X., Simrén J., et al (2021) MDPI AG DOI: 10.3390/ijms222111622	Data available in the supplementary material data
Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape Koenig P., Das H., Liu H., Kümmerer B. M., et al (2021) American Association for the Advancement of Science (AAAS) DOI: 10.1126/science.abe6230	Data generated/analysed are in the article or supplementary materials. data Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U. data Protein Data Bank: 7KN5 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3. data Protein Data Bank: 7KN6 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3. data Protein Data Bank: 7KN7 SARS-CoV-2 spike in complex with nanobodies E. data Protein Data Bank: 7KSG Nanobody E bound to Spike-RBD in a localized reconstruction. data Protein Data Bank: 7B14 SARS-CoV-spike with two RBDs up bound to VHH V on all RBDs. data Protein Data Bank: 7B11 SARS-CoV-spike bound to two neutralising nanobodies. data Protein Data Bank: 7B18 SARS-CoV-spike RBD bound to two neutralising nanobodies. data Protein Data Bank: 7B17 SARS-CoV-2 spike in complex with nanobodies E. data Electron Microscopy Data Bank: EMD-23018 Nanobody E bound to Spike-RBD in a localized reconstruction. data Electron Microscopy Data Bank: EMD-11978 SARS-CoV-spike bound to two neutralising nanobodies. data Electron Microscopy Data Bank: EMD-11981 SARS-CoV-spike RBD bound to two neutralising nanobodies. data Electron Microscopy Data Bank: EMD-11980 Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. data BioProject: PRJNA679438
Natural killer cell immunotypes related to COVID-19 disease severity Maucourant C., Filipovic I., Ponzetta A., Aleman S., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciimmunol.abd6832	Curated flow cytometry data available via the Karolinska COVID-19 Immune Atlas. data Raw data, clinical characteristics of patients, and various results files are available in supplementary data. data
The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China Gao J., Liu J., Wen H., Liu H., et al (2020) Springer Science and Business Media LLC DOI: 10.1186/s12931-020-01363-7	Provided in the article: CT images for 2 patients over 12 days. data