Download


Please cite our preprint on bioRxiv if using TissUUmaps in your work.

Windows installation


Download Windows Installer
Note that the installer is not signed yet and may trigger warnings from the browser and from the firewall. You can safely ignore these warnings.

PIP installation (for Linux and Mac)


  1. Install libvips for your system: https://www.libvips.org/install.html

    An easy way to install libvips is to use an Anaconda environment with libvips:

     conda create -y -n tissuumaps_env -c conda-forge python=3.9 libvips
     conda activate tissuumaps_env
    
  2. Install the TissUUmaps library using pip:
     pip install "TissUUmaps[full]"
    
  3. Start the TissUUmaps user interface:
     tissuumaps
    
  4. Or start TissUUmaps as a local server:
     tissuumaps_server path_to_your_images
    

    And open http://127.0.0.1:5000/ in your favorite browser.

Plugins


You can add plugins to TissUUmaps from the application menu, or by placing plugin files in the folder [USER_FOLDER]/.tissuumaps/plugins/. See here for available plugins.

Server deployment


Static HTML pages

To install TissUUmaps on an Apache web server, follow instructions from https://github.com/TissUUmaps/TissUUmapsCore.

Docker container
  1. Start the docker container cavenel/tissuumaps:latest from Docker Hub:
    docker run -it -p 56733:80 --name=tissuumaps -v /path/to/local/images:/mnt/data cavenel/tissuumaps:latest
    
  2. Place your images in the local folder /path/to/local/images/share.
  3. Open http://127.0.0.1:56733/ in your favorite browser.