imageTCGAutils

imageTCGAutils provides utility functions for working with histopathology images and CONCH data, including coordinate alignment between nuclei segmentation and tile-based pathology models.

Key Features:

• Remote file listing: Lists remote files for CONCH data access.
• Nuclei-tile alignment: Assigns HoverNet nuclei to ProvGigaPath tiles using a scale factor to align coordinates.
• Internal utilities: Provides internal utility functions for the imageFeatureTCGA package.

Scientific Applications:

• Histopathology image analysis: Supports computational pathology workflows by enabling alignment of nuclei segmentations with tile-based feature representations.
• Multi-modal data integration: Facilitates integration of HoverNet nuclear segmentation outputs with ProvGigaPath tile embeddings for downstream analysis.

Methodology:

Coordinate alignment via scale factor application to match HoverNet nuclei positions with ProvGigaPath tile coordinates.