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Minerva Analysis

About

This is an openseadragon based Cellular Image Viewing and Analysis Tool. It is built with a python Flask backend and a Node.js javascript frontend.

Executables (for Users)

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

Running as a Docker container

  • Build image: docker build -t gating .
  • Run image with mounted path: docker run --rm -dp 8000:8000 -v [source path]:/[target path] gating

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. This is necessary in order to import your data via the import page.
  • -dp forwards the port 8000

Once the container is running, go to http://localhost:8000/ in your web browser. To import your imaging files in the import gui type in the mounted /data/..

Clone and Run Codebase (for Developers)

1. Checkout Project

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

2. Checkout Necessary Branch

  • For Gating, run git checkout gating
  • Run git pull to make sure everything is up to date

3. Conda Install Instructions.

Install Conda
  • Install miniconda or conda.
  • Create env: conda env create -f requirements.yml
Activate Environment
  • Active environment: conda activate minerva_analysis
Start the Server
  • python run.py - Runs the webserver
Start the Server
  • Access the tool via http://localhost:8000/

(4. Node.js installation and packages)

This step is only needed when you plan to edit js code. The codebase already included bundled js files.

  • Install Node.js, then navigate to /minerva_analysis/client and run npm install to install all packages listed in package.json.
  • Run npm run start to package the Javascript, or run npm run watch if you plan on editing dependencies

Packaging/Bundling Code as Executable (for Developers)

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

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