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The ST viewer is a tool to visualize spatially resolved gene expression data on top of cell tissue figures with the correct location.

The ST Viewer is cross platform which means that it can be built and run in MAC, UNIX and WINDOWS PCs. The ST viewer allows to interact with the data dynamically. Users can see where specific genes are expressed and how expressed they are. It has different threshold options and many visualization options. It also allows to select areas of the tissue to obtain gene patterns to later do DEA or cell classification.

The ST viewer uses the data generated with the ST Pipeline (link), a pair of tissue images and an alignment matrix (to convert array coordinates to image pixel coordinates).

The ST viewer can access datasets stored in a database trough the ST API (link here) or imported locally with the option "Import dataset" in the Datasets windows (more detailed information about this in the manual).

You can use our public datasets hosted in http://www.spatialtranscriptomicsresearch.org/ if you want to try the ST Viewer.

If you want the ST Viewer to connect and use the data stored in a database trough the ST API you must configure and deploy the ST API, the ST ADMIN and a database. You must then include the server credentials in the configuration file "stviewer.conf". (More information about this will be added to the manual soon).

Read AUTHORS file

Read DEPENDENCIES file

See MANUAL in (link to manual) for more information on how to use the ST Viewer. Currently the manual is a outdated and a new updated manual is being created but many of the main options remain the same.

See LICENSE for the license terms and DEPENDENCIES for the 3rd party libraries that are used in this software.

For the moment we do not generate binaries but you can build the ST Viewer following these instructions :

• Download and install Qt open source from : http://qt-project.org/downloads

• Issue the following to install the necessary dependencies: E.x (Assuming MacPorts is installed, otherwise http://www.macports.org/install.php)

    sudo port install xcode cmake git
  

  NOTE : Make sure the XCode Command Line Tools are installed

• Clone the repository to a specific folder and build the application

    git clone st_viewer_repo /path/to/source
    mkdir /path/to/build
    cd /path/to/build
    cmake [-DCMAKE_INSTALL_PREFIX="/usr/local/bin"] \
      [-DCMAKE_BUILD_TYPE="Debug" | "Release"] \
      [-DCMAKE_PREFIX_PATH="/path/to/qt"] \
      [-DCMAKE_OSX_SYSROOT=”/path/to/macosx.sdk”] \
      [-DCMAKE_OSX_DEPLOYMENT_TARGET=version] \
      [-DPUBLICKEY="path_to_ssl_key"] \
      [-DCONFIG_FILE=”path_to_networl_config_file”]
      /path/to/source
  

  Where :

  DCMAKE_INSTALL_PREFIX = indicates where to install STViewer

  DCMAKE_BUILD_TYPE = indicates the type of building (Release by default)

  DCMAKE_PREFIX_PATH = indicates and extra path to look for packages for example the binaries of Qt5.

  DCMAKE_OSX_SYSROOT = provides the path to the MacOS X SDK that is to be used (Only OSX users) eg: Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/

  DCMAKE_OSX_DEPLOYMENT_TARGET = indicates the target MacOS X version (Only OSX users) eg: 10.7 , 10.8 or 10.9

  DPUBLIC_KEY = In case we want the ST Viewer to access datasets in a database we must give a public key if the API implements HTTPS (this is optional)

  DCONFIG_FILE = In case we want the ST Viewer to access datasets in a database we must give a configuration file with the endpoints and the OAuth access settings. The STViewer will load this file in running time after it is installed so you can also edit the file after installation.

• Build the application

  make -j8 
  

• Run the application typing

    /path/to/build/STViewer.app/Contents/STViewer
  

• Alternatively for MAC you can build a DMG bundle

    make dmg
  

  Then you can use the bundle to install the ST Viewer as an application

• Download and install Qt open source from : http://qt-project.org/downloads

• Issue the following commands

    sudo apt-get install cmake git ubuntu-dev-tools
    sudo apt-get install libglu1-mesa-dev freeglut3-dev mesa-common-dev
  

• Follow from the third step in the OSX guideline except the last step (build and execute)

    make -j8
    make install
  

  To execute type :

    STViewer
  

There are different ways to build the ST Viewer in Windows. We use Cygwin but there are probably easier ways to do it.

• Download and install Qt open source from : http://qt-project.org/downloads

• Install Cygwin, by downloading and executing http://cygwin.com/setup-x86_64.exe

  During the installation, select these additional packages:

  • git (category: Devel)
  • wget (category: Web)
  • openssh (category: Net)

• The CMake included in Cygwin unfortunately doesn’t include the generator for Nmake (-G "NMake Makefiles" ) so you need to install CMake for windows : http://www.cmake.org/cmake/resources/software.html

• Install Microsoft Visual Studio (make sure you install the C++ compilers) : http://www.microsoft.com/visualstudio/eng/visual-studio-2013

• Install NSI installers in Windows : http://nsis.sourceforge.net/Download

• Install OpenSSL

• Build from the source (Currently Qt does not support Visual Studio 2015)

  • You can use the Cygwin based script called build_cygwin.sh to build it from the Cygwin terminal. Make sure the script is configured to the paths of your Visual Studio, Qt and and that the architecture is set to the one in your system (32 or 64) as well as the cmake variables (listed above)

  • Make a directory for the script to copy the build artifacts to. For example ‘st_bin’.

      mkdir st_bin
    

    (When the build has completed this directory will contain the application and it’s installer).

    Then in a Cygwin terminal, for a production build type:

      git clone st_client_repo ~/st_client
      ~/st_client/build_cygwin.sh ~/st_client stclient_production_build st_bin
    

    or for a development build type:

      ~/st_client/build_cygwin.sh  ~/st_client  stclient_development_build  st_bin
    

    At the end of the build script, the paths to the executable and to the package file are printed to the terminal so you can either execute the ST Viewer or install it.