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.
Releases can be found here: https://github.com/labsyspharm/gater/releases These are executables for Windows and MacOS that can be run locally without any installations.
- 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 https://localhost:8000/
in your web browser.
To import your imaging files in the import gui type in the mounted /data/..
git clone https://github.com/labsyspharm/minerva_analysis.git
cd minerva_analysis
- For Gating, run
git checkout gating
- Run
git pull
to make sure everything is up to date
- Active environment:
conda activate minerva_analysis
python run.py
- Runs the webserver
- Access the tool via
https://localhost:8000/
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 runnpm install
to install all packages listed in package.json. - Run
npm run start
to package the Javascript, or runnpm run watch
if you plan on editing dependencies
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}
.