https://github.com/cns-iu/hra-ct-summaries-mx-spatial-data

Cell Type summary files for multiplexed (mx) antibody-based imaging data.
https://github.com/cns-iu/hra-ct-summaries-mx-spatial-data

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Cell Type summary files for multiplexed (mx) antibody-based imaging data.

• Host: GitHub
• URL: https://github.com/cns-iu/hra-ct-summaries-mx-spatial-data
• Owner: cns-iu
• License: mit
• Created: 2023-07-28T18:55:10.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-07-28T20:15:06.000Z (over 1 year ago)
• Last Synced: 2023-07-28T20:24:16.288Z (over 1 year ago)
• Size: 18.6 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# hra-ct-summaries-mx-spatial-data

Cell Type summary files for multiplexed (mx) antibody-based imaging data.

## Directory Description

Each directory in the root directory corresponds to one type of data collection. Within each directory, there are two directories containing CSV files named by HuBMAP IDs of those datasets:

* **cell_coordinates:** This contains all CSVs with individual cell coordinates (x,y) with cell type label. The coordinates belong to cell location within a tissue image.

* **cell_type_counts:** This contains all CSVs with total cell type counts per cell type for each dataset.

## Dataset Description

| Directory Name | Description | Number of HuBMAP Datasets | CT Summary Source | Paper |

| ------------- | ------------- | ------------- | ------------- | ------------- |

| intestine_omap_2_0001 | CODEX Datasets for large and small intestine from John Hickey aligned with OMAP-2| 64 | [Dryad dataset from data provider](https://doi.org/10.5061/dryad.pk0p2ngrf) | [Hickey, J.W., Becker, W.R., Nevins, S.A. et al. Organization of the human intestine at single-cell resolution. Nature 619, 572–584 (2023). https://doi.org/10.1038/s41586-023-05915-x](https://doi.org/10.1038/s41586-023-05915-x) |

| skin_omap_4_0001 | CellDive Datasets for skin from GE Research aligned with OMAP-4| 10 | [Zenodo dataset from data provider](https://doi.org/10.1101/2022.03.30.486438) | [Ghose, S., Ju, Y., McDonough, E. et al. 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging. Commun Biol 6, 718 (2023). https://doi.org/10.1038/s42003-023-04991-z](https://doi.org/10.1038/s42003-023-04991-z) |