CODEX
About the Data
Method and Protocol
Information forthcoming
Data Visualization
Full-resolution images can be viewed in a web browser using Minerva:
- via the gallery (forthcoming)
- in cBioPortal (forthcoming)
Learn more about the Minerva software at minerva.im.
Data Access
All image data will be accessible from Amazon Web Services (AWS):
- Levels 2: QPTIFF
- Level 3: TIFF, CSV
- Level 4: CSV
For a description of the files see the table below.
About the Samples
The following are planned to image with CODEX:
- 5 TMAs
- 50-100 breast samples
Instruments
Information forthcoming
About the Data Generators
This data was generated and analyzed by a team at the lab of Kate Nathanson.
Data Levels:
| Data Type | Description | File Format | Average size (per sample) | Data Location |
|---|---|---|---|---|
| TMA image data (Levels 2) | Quality controlled images are assembled into a high-plex whole slide image | QPTIFF | 5-15 GB | AWS |
| Whole Slide image data (Levels 2) | Quality controlled images are assembled into a high-plex whole slide image | QPTIFF | 50 GB | AWS |
| Segmentation masks (Level 3) | Cell segmentation identifies and separates cell, nucleus, cytoplasm and other regions | TIFF | 0.5 GB | AWS |
| Single-cell spatial feature tables (Level 4) | Summarize the expression of marker intensities and morphological features for each cell | csv | 1 GB | AWS |