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  • High-dimensional imaging of colorectal carcinoma and other tumors with 50+ markers (CRC_FFPE-CODEX_CellNeighs)

Summary

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We have used CODEX to image 56 proteins simultaneously in 140 tissue regions from the tumor invasive front of 35 advanced-stage colorectal cancer (CRC) patients (17 patients with Crohn's-like reaction (CLR) - leading to high amount of tertiary lymphoid structures (TLS); and 18 patients with diffuse inflammatory infiltration (DII) and no TLS). These patients were selected from an initial cohort of 715 CRC patients. Patients with low-stage CRC (pTNM 0-2), pre-operative chemotherapy, insufficient material, and low immune infiltration were excluded. The 35 resulting patients were matched for age, sex and tumor characteristics. CLR patients had a much better survival compared to DII patients.  We expect that making this dataset publicly available will stimulate broad research endeavors into the immune tumor microenvironment of colorectal cancer and allow computational scientists to discover new biomarkers and features. Further details on the study can be obtained in our paper here: https://www.cell.com/cell/fulltext/S0092-8674(20)30870-9

Details on image acquisition and processing:

Automated imaging was performed on a Keyence BZ-X710 microscope using a CFI Plan Apo λ 20x/0.75 objective (Nikon), in high-resolution mode, with a lateral resolution of 377.44 nm/pixel. Processed images labeled with “montage” only have half of that resolution, resulting in a 4x smaller image size (used for stitching of large tissue microarrays).

Acknowledgement

This work would not have been possible without the support and efforts of many individuals and organizations.

  • A complete list of acknowledgements can be found here.


Data Access

Data TypeDownload all or Query/FilterLicense
Tissue Slide Images (TIFF, 2.0TB)


 

(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

CC BY 4.0

Clinical data: Multi-tumor TMA composition (XLS, 13 kB) 


 

CC BY 4.0

Clinical data: CRC TMA patient annotation (XLS, 19 kB) 

 

CC BY 4.0

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Detailed Description

Image Statistics


Modalities

Pathology

Number of Subjects

35

Number of Images

200

Images Size (TB)2.0

High-dimensional CODEX images (hyperstacks of immunofluorescence images)

Citations & Data Usage Policy

Users must abide by the TCIA Data Usage Policy and Restrictions. Attribution should include references to the following citations:

Data Citation

Schürch, C. M., Bhate, S., Barlow, G., Phillips, D., Noti, L., Zlobec, I., Chu, P., Black, S., Demeter, J., McIlwain, D., Samusik, N., Goltsev, Y., & Nolan, G. (2020). High-dimensional imaging of colorectal carcinoma and other tumors with 50+ markers [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2020.FQN0-0326

Publication Citation

Schürch et al., Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front, Cell (2020), https://doi.org/10.1016/j.cell.2020.07.005

TCIA Citation

Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. DOI: 10.1007/s10278-013-9622-7

Other Publications Using This Data

TCIA maintains a list of publications which leverage TCIA data. If you have a manuscript you'd like to add please contact TCIA's Helpdesk.

Version 1 (Current): Updated 2020/08/05

Data TypeDownload all or Query/Filter
Images (TIFF, 2.0TB)


 

Clinical data: Multi-tumor TMA composition (XLS, 13 kB) 


 

Clinical data: CRC TMA patient annotation (XLS, 19 kB) 

 

 



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