Scope2Screen

Scope2Screen is an open-source web-application for focus+context exploration and annotation of whole-slide, high-plex, tissue images. The client -server application consists of a python Flask backend and a Node.js javascript frontend. The server’s restful API allows to retrieve image and feature data and to steer analytics. The frontend is built using Bootstrap, D3.js, and openseadragon, a web-based zoomable imageviewer, which we extend significantly. Take a look at our Wiki to find out more.

Executables (for Users)

Releases can be found here: https://github.com/labsyspharm/scope2screen/releases These are executables for Windows and MacOS that can be run locally without any installations.

Running as a Docker container

From the directory that contains your data files:

docker run --rm -v "$PWD":/data -p 8000:8000 labsyspharm/scope2screen:0.74

where

• --rm cleans up the container after it finishes executing
• -v mounts the "present working directory" (containing your data) to be /data inside the container
• -p forwards the port 8000
• 0.74 specifies the tool version (see Releases)

Once the container is running, go to http://localhost:8000/ in your web browser.

Clone and Run Codebase (for Developers)

Checkout Project

git clone https://github.com/labsyspharm/scope2screen.git

2. Conda Install Instructions.

Install Conda

• Install miniconda or conda.
• Create env: conda env create -f requirements.yml

Activate Environment

• Active environment: conda activate scope2screen

Start the Server

• python run.py - Runs the webserver

Access the Server

• Access the tool via http://localhost:8000/

Packaging/Bundling Code as Executable (for Developers)

Any tagged commit to a branch will trigger a build. This will appear under releases. Note building may take ~10 min.

Tagging Conventions: All release tags should look like v{version_number}_{branch_name}.

• Tagging Example: git tag "vX.X_scope2screen" (adds a tag) followed by git push --tags (pushes the tag)

Publication

This tool prototype is part of the publication: Jared Jessup+#, Robert Krueger+#, Simon Warchol#, John Hoffer#, Jeremy Muhlich#, Cecily C. Ritch, Giorgio Gaglia, Shannon Coy, Yu-An Chen, Jia-Ren Lin, Sandro Santagata, Peter K. Sorger, Hanspeter Pfister, "Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data," in IEEE Transactions on Visualization and Computer Graphics, (to appear in Transaction of Visualization and Computer Graphics, 2021).

+ contributed equally to this work

# have contributed code to the project

Data

To download an example dataset for Scope2Screen, go to https://www.synapse.org/#!Synapse:syn26304730/wiki/613130 and register as a synapse user.