Mantis Viewer is an application developed by the Parker Institute for Cancer Immunotherapy for viewing and analyzing multi-channel pathology imaging, such as IHC, Vectra, MIBI, IMC, CODEX, or other technologies. It has been designed to be highly performant and responsive when analyzing both large and small images and to support workflows with segmentation data.
If you want a walkthrough for using Mantis Viewer, you can check out the documentation!
If you just want to use the application head to the releases page! Otherwise continue reading if you want to build the project yourself or to contribute to this project.
To get up and running for the first time first clone the repository and install the dependencies. You may need to install the build dependencies for canvas first.
npm installOnce NPM has installed all of the dependencies, you can start the application.
npm startWebpack will automatically rebuild the application and restart Electron if you are actively developing.
Running tests is a little funky. It isn't possible to install a version of Node locally that has the same API version as the version of Node that's bundled with Electron. Since this project makes use of native modules, which have to be compiled targeting a specific Node API version, we have to reinstall or recompile the native modules before running tests so they can run using the local Node version, and after running tests so that the modules can be used with Electron's Node version. There's probably a better way to do this, but for now these are the three commands that you need to run tests locally.
npm rebuild
npm run test
npm run postinstallTo generate executables on all systems, you will first need to make sure all dependencies are installed
npm installOnce this is done, you can build and package the application for distribution
Linux:
npm run dist-linuxMac:
npm run dist-macWindows:
npm run dist-winWhen this completes, you should have executables built in the dist directory.
New releases are automatically built on CircleCI and then published to GitHub as drafts. npm-version is used to bump the version.
For a prerelease version run the following command.
npm version prerelease --preid=rcPreminor, minor, and major releases do not need any additional arguments for npm-version.
To specify the verion during a release run the following command
npm version <new-version>Mantis Viewer is build using Electron, Typescript, React, MobX, and PIXI.js.
Please cite Mantis Viewer using the following citation:
Robert Schiemann, Lacey Kitch, Pier Federico Gherardini, Robin Kageyama, & Mike Travers. Mantis Viewer. Zenodo. http://doi.org/10.5281/zenodo.4009579
You may also cite the specific version of Mantis that you used instead if you wish. You can get citations for specific versions on the Mantis Viewer Zenodo Page
Mantis Viewer is distributed under Apache 2 license. See the LICENSE file for details.