labsyspharm/ORION-CRC

This is a companion release for the manuscript, "High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers." 

Nature Cancer: 10.1038/s43018-023-00576-1
bioRxiv: 10.1101/2022.09.28.509927
Visit tissue-atlas.org/atlas-datasets/lin-chen-campton-2023 to view image data (no download required!) and learn more about related work!
The dataset index and scripts for processing and analysis are deposited in the latest release. The same files can also be found on GitHub at github.com/labsyspharm/orion-crc or by following the link under "Related identifiers".
Funding
This work was supported by NCI grants U54-CA225088 and U2C-CA233262 (P.K.S. and S.S.), an NCI SBIR small business grant R41-CA224503 (RareCyte and P.K.S.) and commercial investment from RareCyte; image processing software and data science methods were developed with support from the Bill and Melinda Gates Foundation grant INV-027106 (P.K.S.), a Team Science Grant from the Gray Foundation (P.K.S. and S.S.), the David Liposarcoma Research Initiative (P.K.S. and S.S.), Emerson Collective (P.K.S.) and Ludwig Cancer Research (P.K.S. and S.S.). J.-R.L. is supported by an NCI Research Specialist Award (R50-CA274277), and S.C. by training grants T32-GM007748 from the NIGMS and T32-CA009216 from the NCI. S.S. is also supported by the BWH President's Scholars Award.
Access the full Orion CRC dataset
All images at full resolution, derived image data (e.g., segmentation masks), and single-cell tables are stored and can be accessed through Amazon Web Services (AWS) S3.
AWS S3 bucket location
s3://lin-2023-orion-crc/data
To browse and download the data use either a graphical file transfer application that supports S3 such as CyberDuck, or the AWS CLI tools. A graphical tool may be more convenient but the CLI tools will likely offer higher download speeds. For users who wish to perform processing within AWS, note that the bucket is located in the us-east-1 region so any other resources must be instantiated in this same region.
Cyberduck or Graphical File Transfer Instructions
Make sure anonymous login is selected, either through using the following server information: s3://[e-mail]/ or make sure the anonymous login button is selected.
AWS CLI Tip
Review your IAM permissions and add additional in-line policies, as needed. For example, use: aws s3 ls --no-sign-request s3://lin-2023-crc/data/. If you continue to experience issues using the CLI, please follow the instructions for using a GUI above or refer to AWS existing documentation.
Email tissue-atlas(at)hms.harvard.edu with the subject line "Orion-CRC: Data Access" if you experience issues accessing the above S3 buckets. Please include the steps you have already tried to help us troubleshoot.
File organization
A detailed description of the file organization can be found at github.com/labsyspharm/orion-crc/blob/main/datarelease-README.md