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Spatial Transcriptomics Viewer

The ST viewer is a tool that can be used to visualize and analize spatially resolved gene expression data in 3D (consecutive sections) or in 2D (with the HE stained tissue image).

The ST Viewer is cross platform which means that it can be built and run in OSX, LINUX and WINDOWS.

The ST viewer allows interaction with the data in real time. Users can see where specific genes are expressed and how expressed they are. It has different threshold, normalization and visualization options. It also allows to select areas of the tissue to obtain gene patterns to later do DEA or spot classification using machine learning.

The ST viewer requires as input a matrix of counts in TSV format where genes are columns and spot ids are rows.

The ST viewer requieres also a TSV file with spot coordinates with one of the following formats:

SPOT_X SPOT_Y chip_x chip_y pixel_x pixel_Y

or

SPOT chip_x chip_y pixel_x pixel_y

or

SPOT pixel_x pixel_y

or

SPOT X Y Z 

The first listed format is compatible with the ST Spot Detector and the last format is designed for 3D datasets.

For 2D datasets the HE stained image of the tissue section is required.

For 3D datasets a 3D Mesh object can be provided.

Loading a dataset

If you want to load a dataset you can go to the "Datasets view" and click in the button "Import dataset" then a dialog form will be shown where you can load the matrix of counts, the HE image and other files. You can also upload a dataset automatically if its files are inside a folder with the option "Load folder" or you can use a meta-file to load a dataset. The meta-file must describe where all the dataset's files are and it should have the following JSON format:

{
    	"name": "test",
    	"comments": "test_comments",
	"data": "/Users/user/test_dataset/stdata.tsv",
	"image": "/Users/user/test_dataset/image.jpg",
	"coordinates": "/Users/user/test_dataset/spots.txt",
}

After that you can just double click in the dataset to open it. (more detailed information about this in the wiki).

Authors

Read AUTHORS file

Dependencies

Read DEPENDENCIES file

Manual

See Wiki

License

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

Contact

For any question/bugs/feedback you can contact Jose Fernandez Navarro jc.fernandez.navarro@gmail.com

Binaries (Install from binaries)

Binaries (installers) for MAC and Windows are provided in the "Releases" tab. To install the ST Viewer using the installers follow these intructions:

OSX

The binary provided for MAC requires OSX 10.5 or bigger.

  • Download the installer (DMG) open it and drag the ST Viewer icon to Applications and then the ST Viewer will be installed in your system.
Windows
  • Download the Windows installer double click on it and follow the instructions, once done the ST Viewer will be installed in your system.

Docker container

This has been tested on a Linux Ubuntu 17.04 as host system.

Build the image:

docker build . -t st_viewer

Launch the image, mounting also the volume where you have the dataset. For example if your dataset is in /home/user/STDatasets/ you need to launch with the option -v /home/user/STDatasets:/STDatasets which you can then find, via the fileBrowser of the Viewer in the directory /STDatasets. Note that you need to allow the root user to use your Display to see the Viewer:

xhost +local:root

Then launch the image according to where your file are located.

docker run -d -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix:rw -v /home/user/STDatasets:/STDatasets st_viewer

Building from the source

  • Download and install CMake

  • Download and install Qt open source from http://qt-project.org/downloads (Choose Desktop application and Open Source and then use the default settings and location). For Windows you must choose the mingw64 option and include QT Charts for every platform.

  • Download and extract QCustomplot from http://www.qcustomplot.com

  • Download and build Armadillo from http://arma.sourceforge.net/download.html

    NOTE (Armadillo only needs to be built for Linux and OSX, for Windows you just need to download and extract it to a folder):

    • Download the latest stable release and then open a terminal and type (x.xxx.x refers to the Armadillo version):

        tar -xvf armadillo-x.xxx.x.tar.xz
        cd armadillo-x.xxx.x
        ./configure
        make
      
OSX
  • Make sure that XCode and XCode Command Line Tools are installed (check by typing "xcode-select" on a terminal) If needed to you can install them from the Apple store (https://developer.apple.com/xcode/). I recommend to update to the latest version of XCode.

  • Make sure to have installed OpenMP, for example with "brew install libomp"

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

      git clone https://github.com/jfnavarro/st_viewer.git
      mkdir st_viewer_build
      cd st_viewer_build
      cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="/path/to/libraries" -DCMAKE_OSX_SYSROOT="/path/to/macosx.sdk" -DCMAKE_OSX_DEPLOYMENT_TARGET=version ../st_viewer
    

    Where :

    DCMAKE_BUILD_TYPE = indicates the type of building ("Debug" or "Release" which is the default)

    DCMAKE_PREFIX_PATH = the path to where Qt, armadillo and qcustomplot are installed

    eg: "/Users/username/Qt/5.14.1/clang_64;/path/to/qcustomplot;/Users/username/armadillo"

    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/MacOSX10.15.sdk/

    DCMAKE_OSX_DEPLOYMENT_TARGET = use 10.15 for example

  • Compile the application

    make -j4 
    
  • Run the application by clicking on the STViewer.app icon that can be found in

      /st_viewer_build
    
Linux

If you are on a Ubuntu, you can use the ubuntu_dep_and_compile.sh to install the dependencies and compile the code with:

sudo ubuntu_dep_and_compile.sh

Or you can follow the process outlined below.

  • Issue the following commands (Ubuntu, for Fedora you must use yum)

      sudo apt-get install git ubuntu-dev-tools
      sudo apt-get install libglu1-mesa-dev freeglut3-dev mesa-common-dev
    
  • Clone the repository to a specific folder and build the application

      git clone https://github.com/jfnavarro/st_viewer.git
      mkdir st_viewer_build
      cd st_viewer_build
      cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="/path/to/libraries" ../st_viewer
    

    Where :

    DCMAKE_BUILD_TYPE = indicates the type of building ("Debug" or "Release" which is the default)

    DCMAKE_PREFIX_PATH = the path to where Qt, armadillo and qcustomplot are installed

    eg: "/Users/username/Qt/5.14.1/gcc;/Users/username/qcustomplot;/Users/username/armadillo"

  • Then type the following to build and install

      make -j4
      make install
    
  • To execute type :

      STViewer
      or
      /path/to/bin/STViewer
    

Note that for Linux you may want to update your LD_LIBRARY_PATH variable to contain the R and QT paths

eg: LD_LIBRARY_PATH=/usr/lib/R/lib/:/home/username/Qt/5.14.1/gcc_64/lib
Windows
  • Download and install Git for windows from https://git-scm.com/downloads

  • Open the GIT terminal and clone the repository :

      git clone https://github.com/jfnavarro/st_viewer.git
    
  • Install MinGW64 with multi-threading (OpenMP and threads) support (http://mingw-w64.org/doku.php)

  • Make sure that your PATH environment variable contains MinGW's paths

      eg PATH=C:\MinGW;C:\MinGW\bin;C:\MinGW\lib
    
  • Make sure that you do not have another MinGW in your PATH variable

  • Open a windows terminal (cmd.exe)

  • Type the following

      mkdir build
      cd build
      cmake -G "MinGW Makefiles" -DCMAKE_SH="CMAKE_SH-NOTFOUND" -DCMAKE_BUILD_TYPE="Release" -DCMAKE_PREFIX_PATH="/path/to/libraries" -DARMADILLO_PATH="C:\\armadillo" ../st_viewer
    

    Where:

    DCMAKE_BUILD_TYPE = indicates the type of building ("Debug" or "Release" which is the default)

    DCMAKE_PREFIX_PATH = the path to where Qt and qcustomplot are installed

    eg: "C:\Qt\5.14.1\mingw53_64;C:\qcustomplot"

    DARMADILLO_PATH = indicates where armadillo was extracted

    eg: "C:\armadillo"

    ../st_viewer = is the path where the ST Viewer was cloned/downloaded

  • Now build and install the ST Viewer by typing (you must run this as an administrator):

      mingw32-make install
    
  • By default the ST Viewer will be installed in "Program Files" but that can be changed with the CMake variable -DCMAKE_INSTALL_PREFIX (it is recommended to install the ST Viewer as an administrator)