CellPhe Dashboard

A dashboard for the CellPhe cell phenotyping library.

Usage

The dashboard is run locally so that you are in full control of your images and do not need to upload them anywhere. It is cross-platform and runs in a web browser and doesn't require any coding experience beyond that required to run the CellPhe python package.

Prerequisites

The only prerequisite is to install Docker (or Docker Desktop for Windows users). Optionally you can run the dashboard from the source code, although this is more involved and slower as it requires manually installing the dependencies. However, if you are unable to install Docker on your computer due to the elevated permissions it needs to run, then this might be necessary.

Running with Docker

Simply download the Docker image from this repository by running the following command in a terminal or command prompt:

docker pull ghcr.io/uoy-research/cellphe-dashboard:main

Then run it:

docker run --rm -p 8501:8501 ghcr.io/uoy-research/cellphe-dashboard:main

You can then access the app by navigating to http://127.0.0.1:8501/ in a web-browser.

Running from source

The app can be run without Docker, although it will require installing the dependencies by hand which takes some time. NB: Currently Python 3.12 is the supported version, other versions may require tweaking the Python dependencies.

The tracking functionality depends on the ImageJ plugin TrackMate, which in turn depends on having a Java runtime available. We recommend the Eclipse Temurin variant, which is built on OpenJDK and is free, stable, and widely supported.

1. Download: Go to the Adoptium Temurin website.
2. Select & Install:
   • Windows: Click the "Latest LTS Release" button. Run the downloaded .msi file and follow the prompts. (Ensure the "Set JAVA_HOME variable" option is checked during installation).
   • macOS: Download the .pkg file for your chip type (Apple Silicon or Intel). Open it and follow the installation prompts.
   • Linux (Debian/Ubuntu): Open a terminal and run the following (NB: you can also install Canonical's build from the openjdk-21-jdk package)

     sudo apt update
     sudo apt install temurin-21-jdk

After installing, open a new terminal/command prompt and run:

java -version

If you see the version details, your Java installation is successful and you are ready to setup the Python environment. Firstly, clone this repository and change into it:

git clone https://github.com/uoy-research/CellPhe-dashboard.git
cd CellPhe-dashboard

Then install the Python prequisites, ideally in a new virtual environment:

pip install -r requirements.txt

Then you can run the app although NB: the first time tracking is run it will take some time to setup an ImageJ instance.

streamlit run CellPheDashboard.py --server.port=8501 --server.address=0.0.0.0