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1 | 1 | # Obtaining the datasets |
2 | 2 |
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3 | | -The example notebooks operate on a set of spatial omics datasets that can be downloaded and converted to Zarr (OME-NGFF) with the scripts available in https://github.com/giovp/spatialdata-sandbox. |
| 3 | +Here you can find all datasets necessary to run the example notebooks already converted to the ZARR file format. |
4 | 4 |
|
5 | | -Here you can find the dataset hosted in S3 object storage. |
| 5 | +If you want to convert additional datasets check out the scripts available in the [spatialdata sandbox](https://github.com/giovp/spatialdata-sandbox). |
6 | 6 |
|
7 | | -| Dataset | .zarr.zip | S3 (see note below!) | |
8 | | -| :------------------------------------------------------------------------------------------------------------------------------------------------------: | :----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: | |
9 | | -| cosmx_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr> | |
10 | | -| mcmicro_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr> | |
11 | | -| merfish | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr> | |
12 | | -| mibitof | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr> | |
13 | | -| steinbock_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr> | |
14 | | -| toy | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr> | |
15 | | -| visium | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zarr> | |
16 | | -| visium_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zarr> | |
17 | | -| visium_associated_xenium_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr> | |
18 | | -| xenium_rep1_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zarr> | |
19 | | -| xenium_rep2_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr> | |
20 | | -| [additional resources for methods developers](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/developers_resources/storage_format/) | - | - | |
| 7 | +| Technology | Sample | Filename | File Size | download data | work with data remotely [^1] | |
| 8 | +| :--------------------- | :------------------------- | :-------------------------- | --------: | :---------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------------- | |
| 9 | +| NanoString CosMx | Non-small cell lung cancer | cosmx_io | 4.2 GB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr/) | |
| 10 | +| CyCIF | Breast Cancer | mcmicro_io | 250 MB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr/) | |
| 11 | +| MERFISH | Mouse Brain | merfish | 50 MB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr/) | |
| 12 | +| MIBI-TOF | Colorectal Cancer | mibitof | 25 MB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr/) | |
| 13 | +| Imaging Mass Cytometry | 4 different cancers | steinbock_io | 820 MB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr/) | |
| 14 | +| Visium | | visium | 61 MB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zarr/) | |
| 15 | +| Visium | | visium_io | 190 MB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zarr/) | |
| 16 | +| Visium | Breast Cancer | visium_associated_xenium_io | 1.5 GB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr/) | |
| 17 | +| Xenium | Breast Cancer | xenium_rep1_io | 2.8 GB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zarr/) | |
| 18 | +| Xenium | Breast Cancer | xenium_rep2_io | 3.7 GB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr/) | |
| 19 | +| | | toy | 11 kB | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr/) | |
21 | 20 |
|
22 | | -## Note |
23 | | - |
24 | | -Opening the above URLs in a web browser would not work, you need to treat the URLs as Zarr stores. For example if you append `/.zgroup` to any of the `.zarr` URLs above you will be able to see that file. |
| 21 | +[^1]: Opening the S3 URLs in a web browser will not work, you need to treat the URLs as Zarr stores. For example if you append `.zgroup` to any of the URLs above you will be able to see that file. |
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