|
1 | | -# Obtaining the datasets |
2 | | - |
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. |
4 | | - |
5 | | -Here you can find the dataset hosted in S3 object storage. |
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/) | - | - | |
21 | | - |
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. |
| 1 | +# Spatial omics datasets |
| 2 | + |
| 3 | +Here you can find all datasets necessary to run the example notebooks already converted to the ZARR file format. |
| 4 | + |
| 5 | +If you want to convert additional datasets check out the scripts available in the [spatialdata sandbox](https://github.com/giovp/spatialdata-sandbox). |
| 6 | + |
| 7 | +| Technology | Sample | File Size | Filename | download data | work with data remotely (**see note below**) | license | |
| 8 | +| :---------------------------------------- | :-------------------------------------------------------- | ------------------------------: | :-------------------------- | :---------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------------- | :---------------------------------------------------------------------- | ----------------------------------- | |
| 9 | +| Visium | Breast Cancer [^2] | 1.5 GB | visium_associated_xenium_io | [.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/) | CCA | |
| 10 | +| Xenium | Breast Cancer [^2] | 2.8 GB | xenium_rep1_io | [.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/) | CCA | |
| 11 | +| Xenium | Breast Cancer [^2] | 3.7 GB | xenium_rep2_io | [.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/) | CCA | |
| 12 | +| CyCIF (MCMICRO output) | Small lung adenocarcinoma [^3] | 250 MB | mcmicro_io | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr/) | CC BY-NC 4.0 DEED | |
| 13 | +| MERFISH | Mouse Brain [^4] | 50 MB | merfish | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr/) | CC0 1.0 DEED | |
| 14 | +| MIBI-TOF | Colorectal carcinoma [^5] | 25 MB | mibitof | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr/) | CC BY 4.0 DEED | |
| 15 | +| Imaging Mass Cytometry (Steinbock output) | 4 different cancers (SCCHN, BCC, NSCLC, CRC) [^6][^7][^8] | 820 MB | steinbock_io | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr/) | CC BY 4.0 DEED | |
| 16 | +| <!-- | NanoString CosMx | Non-small cell lung cancer [^1] | 4.2 GB | cosmx_io | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr/) | NanoString removed the dataset? --> | |
| 17 | + |
| 18 | +**Note on S3 storage:** 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. |
| 19 | + |
| 20 | +## Licenses abbreviations |
| 21 | + |
| 22 | +- CCA: Creative Common Attribution |
| 23 | +- CC0 1.0 DEED: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication |
| 24 | +- CC BY 4.0 DEED: Creative Common Attribution 4.0 International |
| 25 | +- CC BY-NC 4.0 DEED: Creative Common Attribution-NonCommercial 4.0 International |
| 26 | + |
| 27 | +<!-- to add: raccoon, blobs, "additional resources for methods developers" --> |
| 28 | +<!-- Artificial datasets |
| 29 | +| Description | File Size| Filename | download data | work with data remotely [^1] | |
| 30 | +| :--------------------- | :------------------------- | --------:| :-------------------------- | :---------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------------- || - | - | 11 kB| toy | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr/) | --> |
| 31 | + |
| 32 | +# Artificial datasets |
| 33 | + |
| 34 | +Also, here you can find [additional datasets and resources for methods developers](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/developers_resources/storage_format/). |
| 35 | + |
| 36 | +# References |
| 37 | + |
| 38 | +Please .. |
| 39 | +[^1]: He, S. et al. High-Plex Multiomic Analysis in FFPE Tissue at Single-Cellular and Subcellular Resolution by Spatial Molecular Imaging. bioRxiv 2021.11.03.467020 (2021) doi:10.1101/2021.11.03.467020. |
| 40 | +[^2]: Janesick, A. et al. High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue. bioRxiv 2022.10.06.510405 (2022) doi:10.1101/2022.10.06.510405. |
| 41 | +[^3]: Schapiro, D. et al. MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging. Cold Spring Harbor Laboratory 2021.03.15.435473 (2021) doi:10.1101/2021.03.15.435473. |
| 42 | +[^4]: Moffitt, J. R. et al. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science 362, (2018). |
| 43 | +[^5]: Hartmann, F. J. et al. Single-cell metabolic profiling of human cytotoxic T cells. Nat. Biotechnol. (2020) doi:10.1038/s41587-020-0651-8. |
| 44 | +[^6]: Windhager, J., Bodenmiller, B. & Eling, N. An end-to-end workflow for multiplexed image processing and analysis. bioRxiv 2021.11.12.468357 (2021) doi:10.1101/2021.11.12.468357. |
| 45 | +[^7]: Eling, N. & Windhager, J. Example imaging mass cytometry raw data. (2022). doi:10.5281/zenodo.5949116. |
| 46 | +[^8]: Eling, N. & Windhager, J. steinbock results of IMC example data. (2022). doi:10.5281/zenodo.7412972. |
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