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Minerva Repository Structure

Code style: black

Minerva Story

The GitHub Pages site build is stored at minerva-story. The source code for the minified bundle is stored at minerva-browser.

Minerva Author

The Python Flask server along with automated testing is stored at minerva-author. The React UI is stored at minerva-author-ui

Using Minerva Author

Installing

All commands should be run in "Terminal" on MacOS and "Anaconda Prompt" on Windows.

First, download this repository through the git command line:

git clone https://github.com/labsyspharm/minerva-author.git

Windows

MacOS

Then run the following commands to set up the development environment:

cd minerva-author
git submodule update --init --recursive
conda config --add channels conda-forge
conda create --name author python=3.8 nomkl
conda activate author
pip install numpy
conda env update -f requirements.yml
conda install openslide
conda install scikit-image
conda install zarr

Running

python src/app.py
  • Browser window should open automatically, if not then open a browser to localhost:2020

  • Browse or copy the file path to an OME-TIFF or SVS

  • Click import and wait for the generation of a full pyramid

At minimum, you'll need to type one 'Group' name into the top dropdown to create a group. For each group you create, you can select channels from the second dropdown and set up their rendering settings with the various sliders. After you hit 'save', look in the directory of the executable (or app.py) for a new folder which contains the generated Minerva Story, with configuration files and an image pyramid.

Automated test suite

The project contains automated tests using the pytest framework. To run the test suite, simply execute in the project folder:

pytest

Automated Releases

All pushes to master will update the current draft relase.

Packaging

MacOS

To package the application as a standalone executable, run script:

bash package_mac.sh

Windows (powershell)

Fetch OpenSlide binaries from https://openslide.org/download/#windows-binaries and save the .dll files to /src. Then run script:

package_win.bat

About

Tool to create images and configuration files for Minerva-Story

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