Quickly tile whole-slide scans into pyramidal images for holistic image review and data-driven decision-making in highly-multiplexed tissue imaging.

What it does

quick-look is a command-line tool that processes whole-slide scans from RareCyte imagers (.rcpnl files) and converts them into pyramidal OME-Zarr images. This format is ideal for fast, interactive viewing of very large images, as it allows visualization clients to load only the visible parts of the image at the appropriate resolution.

NOTE: Whole-slide scans from RareCyte imagers are supported. Processing file formats from other vendors is feasible but is not supported at the moment.

Key features

• Converts .rcpnl files to multi-scale OME-Zarr.
• Processes a directory of scans or monitors a directory for new scans to process automatically.
• Extracts channel names from .rcjob files if present.

Installation

We recommend using pixi for environment management.

1. Create a pixi workspace & install quick-look:

   mkdir quicklook-env
   cd quicklook-env
   
   # Download pixi configuration
   curl -OL https://raw.githubusercontent.com/Yu-AnChen/quick-look/main/pixi/pixi.toml
   curl -OL https://raw.githubusercontent.com/Yu-AnChen/quick-look/main/pixi/pixi.lock
   
   # Install dependencies
   pixi install

2. Activate the environment:

   When using pixi, prepend pixi run to all quicklook commands. For example: pixi run quicklook process --help.

Usage

quick-look provides two main commands: process to convert a directory of scans, and monitor to watch a directory for new scans.

Process a directory of scans

The process command will process all compatible files/folders in the specified input directory.

quicklook process -i <path/to/input/directory> -o <path/to/output/directory>

The input directory can contain:

• .rcpnl files.
• Folders, each containing one .rcpnl file and optionally one .rcjob file (for channel names).
• On Windows, shortcuts to the above files and folders are also supported.

Example:

Given this input directory, containing 1 rcpnl file and a folder with an rcpnl file in it:

C:\quick-look\input
│   LSP001@20230922_142033_633584.rcpnl
│
└───LSP002@20230922_200722_567967
        LSP002@20230922_200722_567967.rcjob
        LSP002@20230922_200722_567967.rcpnl

Running this command:

quicklook process -i C:\quick-look\input -o C:\quick-look\output

Will produce two OME-Zarr folders in the output directory:

C:\quick-look\output
├───LSP001@20230922_142033_633584.ome.zarr
└───LSP002@20230922_200722_567967.ome.zarr

Monitor a directory for new scans

The monitor command watches a directory and automatically processes new scans as they are added. This is useful for automated processing pipelines.

quicklook monitor -i <path/to/input/directory> -o <path/to/output/directory>

The tool will watch the input directory and, when a new file, folder, or Windows shortcut is added, it will launch the tiling process and write the result to the output directory.

Viewing the output

The generated .ome.zarr files can be viewed with various tools that support the NGFF format. We recommend using QuPath v0.6.x.

Other tools that can open NGFF images are listed at NGFF documentation.