img2tiff

Convert image to OME-TIFF format (pyramid, JPEG pending). Tested on QuPath 0.6.0 under macOS, both arm64 and x86 emulated, in headless mode.

Nextflow Workflow

Parameters:

• input_folder: URI to folder which contains the images to convert
• image_format: File suffix for images which will be converted
• output: Folder where results will be published
• container: Docker container used to run QuPath (default: 'public.ecr.aws/cirrobio/qupath:0046339')

Behavior: Any file within input_folder which has the image_format suffix will be provided as an input to the img2tiff_headless.groovy script within QuPath. Every independent series within each image will be written out as a separate OME-TIFF file.

Standalone Script: img2tiff_headless.groovy

Arguments:

• param1: input image path
• param2: series number (optional, defaults to 1)

The H&E images we work with have at least four series:

0. Slide Label
1. Medium resolution overview
2. Full resolution (e.g. 40X brightfield)

The full resolution image seems to take around 10 minutes to convert an image on 2 cores of an M1 Apple Silicon MacBook Pro.