Code repo for ImageAnalysisR project.

HoVerNet:

ProvGigaPath:

file html: Ovarian Cancer Purity Analysis

To populate the wsi_image folder with TCGA images, follow these steps:

## Make sure BiocManager is installed
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## Make sure GenomicDataCommons is installed
# BiocManager::install("GenomicDataCommons")
library("GenomicDataCommons")

# File IDs to download
file_ids <- c(
# Insert your file IDs here
  )

# Download files
lapply(file_ids, gdcdata)

To use HoVerNet for segmentation:

1. Set up the Conda environment as described in the HoverNet GitHub repository.
2. Run the script run_infer.sh in a GPU-enabled environment. The output will be a JSON file containing the nuclei segmentation and classification results.

To extract features from the HoVerNet segmentation output (JSON file):

• Use the scripts hovernet_py.qmd to process the JSON file and generate an .h5ad file.

In this folder you can find example for:

• HoVerNet output in .json, mask in .png, thumb in .png
• Features Extraction output in .h5ad.

• Annual Review on Digital Pathology
• Scientific Review on Digital Pathology

• arXiv: Systematic Evaluation of Cell Segmentation Algorithms

• Paper using HoVerNet outputs: PMCID: PMC10985477
• Original HoVerNet paper: HoVerNet
• HoVerNet GitHub repository: GitHub - HoverNet
• HoVerNext paper: HoVerNext
• HoVerNext GitHub repository: GitHub - HoverNext

• UNI Benchmarks

• UNI:
  • Paper: Nature Medicine - UNI
  • GitHub: GitHub - UNI
• Prov-GigaPath:
  • Paper: Nature - Prov-GigaPath
  • GitHub: GitHub - Prov-GigaPath

• TCGA Repository
• TCIA Repository

• ImageAnalysisR (Shared Code/Material)
• imageTCGA (Shiny Package)
• TCIAAPI (R Package)

• EBImage:
  • EBImage
  • GitHub: EBImage
• MSIreg:
  • Paper: Oxford Bioinformatics - MSIreg
  • GitHub: MSIreg