TissUUmaps 3.0.8.11

TissUUmaps is a lightweight viewer that uses basic web tools to visualize gene expression data or any kind of point data on top of whole slide images.

TissUUmaps - UU is for Uppsala University ;)

TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.

Windows installation

1. Download the Windows Installer from the last release and install it. Note that the installer is not signed yet and may trigger warnings from the browser and from the firewall. You can safely pass 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.

Image format

TissUUmaps can read whole slide images in any format recognized by the OpenSlide library:

• Aperio (.svs, .tif)
• Hamamatsu (.ndpi, .vms, .vmu)
• Leica (.scn)
• MIRAX (.mrxs)
• Philips (.tiff)
• Sakura (.svslide)
• Trestle (.tif)
• Ventana (.bif, .tif)
• Generic tiled TIFF (.tif)

TissUUmaps will convert any other format into a pyramidal tiff (in a temporary .tissuumaps folder) using vips.

If your image fails to open, try converting it to tif format using an external tool.