Minerva Repository Structure
Using Minerva Author
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
- Microsoft C++ Build Tools
- Install Anaconda
- Move openslide "bin" directory to "minerva-author/src"
conda install -c anaconda git
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
Browser window should open automatically, if not then open a browser to
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:
All pushes to master will update the current draft relase.
To package the application as a standalone executable, run script:
Fetch OpenSlide binaries from https://openslide.org/download/#windows-binaries and save the .dll files to /src. Then run script: