LazySlide with nextflow for WSI preprocessing

The script offers

• Find tissue + Tile tissue
• QC tisssue and tiles
• Feature extraction (multiple models)
• Aggregation of features

Usage

1. Install LazySlide

Make sure lazyslide is available in your current shell environment.

Try to execute lazyslide to see if it's available.

2. Install nextflow

See the offical website

Or you can install with conda or mamba conda install bioconda::nextflow

3. Setup sample data (optional)

Clone this repo:

git clone xxx

Assume you are in the root of the repo, now run

sh scripts/setup_sample_data.sh your_data_dir
# Or you can have a larger dataset
sh scripts/setup_gtex_gastris_data.sh your_data_dir

4. Run the script

nextflow run rendeirolab/lazyslide-nextflow 
    \ --input your_data_dir/input.csv 
    \ --tile_px 256 
    \ --models 'alexnet,resnet50,uni'