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‎datasets/README.md

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# Obtaining the datasets
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# Spatial omics datasets
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Here you can find all datasets necessary to run the example notebooks already converted to the ZARR file format.
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If you want to convert additional datasets check out the scripts available in the [spatialdata sandbox](https://github.com/giovp/spatialdata-sandbox).
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| Technology | Sample | File Size | Filename | download data | work with data remotely [^1] |
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| :---------------------------------------- | :--------------------------------------------------- | --------: | :-------------------------- | :---------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------------- |
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| 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/) |
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| 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/) |
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| 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/) |
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| 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/) |
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| 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/) |
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| 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/) |
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| 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/) |
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| 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/) |
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| Technology | Sample | File Size | Filename | download data | work with data remotely (**see note below**) | license |
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| :---------------------------------------- | :-------------------------------------------------------- | ------------------------------: | :-------------------------- | :---------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------------- | :---------------------------------------------------------------------- | ----------------------------------- |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| <!-- | 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? --> |
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**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.
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## Licenses abbreviations
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- CCA: Creative Common Attribution
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- CC0 1.0 DEED: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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- CC BY 4.0 DEED: Creative Common Attribution 4.0 International
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- CC BY-NC 4.0 DEED: Creative Common Attribution-NonCommercial 4.0 International
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<!-- to add: raccoon, blobs, "additional resources for methods developers" -->
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<!-- Artificial datasets
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| Description | File Size| Filename | download data | work with data remotely [^1] |
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| :--------------------- | :------------------------- | --------:| :-------------------------- | :---------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------------- || - | - | 11 kB| toy | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip) | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr/) | -->
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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/).
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# Artificial datasets
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[^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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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/).
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# References
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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.
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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.
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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.
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4. Moffitt, J. R. et al. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science 362, (2018).
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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.
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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.
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7. Eling, N. & Windhager, J. Example imaging mass cytometry raw data. (2022). doi:10.5281/zenodo.5949116.
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8. Eling, N. & Windhager, J. steinbock results of IMC example data. (2022). doi:10.5281/zenodo.7412972.
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Please ..
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[^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.
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[^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.
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[^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.
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[^4]: Moffitt, J. R. et al. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science 362, (2018).
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[^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.
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[^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.
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[^7]: Eling, N. & Windhager, J. Example imaging mass cytometry raw data. (2022). doi:10.5281/zenodo.5949116.
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[^8]: Eling, N. & Windhager, J. steinbock results of IMC example data. (2022). doi:10.5281/zenodo.7412972.

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