Searching for image data

Hi all,

I’m searching for a covid-19 related source of image data. E.g. publications with supplemental material. Has anyone found something like this? I only found small databases and individual images

X-Ray / Computed tomography (screenshots)
https://github.com/ieee8023/covid-chestxray-dataset]
https://www.sirm.org/category/senza-categoria/covid-19

Electron microscopy
https://phil.cdc.gov/Details.aspx?pid=23336
https://phil.cdc.gov/Details.aspx?pid=23354
https://www.nejm.org/doi/suppl/10.1056/NEJMc2001899/suppl_file/nejmc2001899_appendix.pdf

Thanks!

Cheers,
Robert

4 Likes

Here is another CT dataset related to COVID19 patients: https://github.com/UCSD-AI4H/COVID-CT
looking inside, you notice that is super unorganized and yields png images of about 220x150 pixels. But it can be a start.

1 Like

Cross posting (original by the OME team)

Data for Lamers et al. showing SARS-CoV-2 in intestinal organoids now available in the the IDR.

covid19

The dataset is available as idr0083. For close up views of the viruses, see:

along with the other ROIs.

The 2 30GB images have also been converted to Zarr with bioformats2raw and are available via public S3 thanks to EMBL-EBI at:

Screen Shot 2020-05-01 at 10.29.24

with the layout as specified in https://github.com/ome/omero-ms-zarr/blob/08f9c8a07194cc0c3da16c95682fee9f0ba46bf5/spec.md :

    ├── .zgroup               # Each image is a Zarr group with multscale metadata.
    └── 0                     # Each multiscale level is stored as a separate Zarr array.
        ├── .zarray           #
        ├── 0.0.0.0.0         # Chunks are stored with the flat directory layout.
        └── t.c.z.y.x         # All image arrays are 5-dimensional
                              # with dimension order (t, c, z, y, x).

The @OMETeam