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TABLE OF CONTENTS

  • GENERAL INFORMATION
    • TITLE
    • AUTHORS AND BEST CONTACT
    • RECOMMENDED CITATION
    • LICENSES
    • USEFUL LINKS
  • DATE OF DATA COLLECTION
  • FILE ORGANIZATION
  • FUNDING
  • ADDITIONAL NOTES/COMMENTS

Note: If you are viewing on Zenodo, please check the GitHub link for updates to this file.

GENERAL INFORMATION

  1. Publication or Dataset Title:

  2. Authors:

  3. Contact Information

  • Name:
  • Organization/institution:
  • Email:

  1. Links to publications that cite or use the data: <include DOI and APA citation to publications that use this data, if applicable>

  2. Recommended citation for this dataset:

  1. Licenses/restrictions placed on the data: <e.g. CC BY https://creativecommons.org/licenses/by/4.0/>

  2. For more information, go to:

FILE ORGANIZATION

  1. FILE NAMING CONVENTIONS:
    Each file follows the following naming convention:

  2. FILE TYPES/SUMMARY: Each folder corresponds to a patient sample (N). The following files are available for each patient and are located on [Synapse/AWS/Etc].

File Type Description Location
N.ome.tif Stitched multiplex CyCIF image pyramid in ome.tif format AWS
N_HE.vsi Hematoxylin and Eosin stained image of adjacent FFPE tissue section in .vsi format AWS
_N_HE_/ folder: raw image data accompanying .vsi file AWS
markers.csv list of all markers in ome.tif image Synapse
N.csv single-cell feature table, including intensity data for all channels Synapse
N_ROI.csv X and Y coordinates for histologically annotated regions in CyCIF and H&E images Synapse
raw/ folder of raw IF image data in .rcpnl format AWS
segmentation/ folder of segmentation maps for tissue image in .tif format AWS

Synapse Library: Edit this to link directly to your public Synapse Library

Free account registration is required to download files from Synapse.

Images and metadata are available in the bucket at the following AWS location: [ADD BUCKET DETAILS]

Files available through AWS S3 are made available using a “requester pays” model.
The person downloading the data must have an AWS account, and AWS will charge the user's account $0.10/GB for downloading all or part of the data.

Note About Accessing AWS 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. Please refer to the documentation for your chosen tool on how to sign in and enable access to requester-pays buckets. There is unfortunately no web-browser-based mechanism for accessing a requester-pays bucket. Keep in mind the download costs, which will run over $200 for downloading one copy of the entire dataset. For users who wish to perform processing within AWS to avoid transfer charges, note that the bucket is located in the us-east-1 region so any other resources must be instantiated in this same region.

  1. FILE LIST <list all files (or folders, as appropriate for dataset organization) contained in the Synapse repository, with a brief description>

N.ome.tif

Patient File Name Location File size
ID ID.ome.tif AWS 90.6 GB

N_HE.vsi

Patient File Name Location File size
ID ID.ome.tif_HE.vsi AWS 531.2 KB

_N_HE_/

Patient File Name Location File size
ID frame_t.ets AWS 928.7 MB

markers.csv

Patient File Name Synapse ID File size
ID markers.csv syn12345678 530 bytes

N.csv

Patient File Name Synapse ID File size
ID ID.csv

N_ROI.csv

Patient File Name Synapse ID File size
ID ID_ROI.csv

raw/

Patient Number of Files Folder size Location
ID 13

segmentation/

Patient Number of Files Folder size Location
ID

FUNDING

Please add relevant funding details

ADDITIONAL NOTES/COMMENTS

Please let (Name, contact information) know if any errors are found in this data.