Download

  The public version of cellXpress is fully functional and free for non-commercial research and educational purposes only. Please contact us if you would like to get a license for commerical applications.

  Please check the before downloading.

    Operating systems
  • 64-bit Windows 11 and 10
  • 32-bit systems are not supported
    Processors
  • Minimum: Intel (Sandy Bridge) or AMD (Bulldozer) CPUs with AVX support
  • Recommended: Intel (Skylake) or AMD (Ryzen 1000) CPUs with AVX2 support
  • Support multi-core processors
    Graphics Processing Unit (for CSAI acceleration)
  • Minimum: GeForce GTX 1050, NVIDIA TITAN X
  • Recommended: Geforce RTX 3060 or above
  • Please make sure you update to the latest NVIDIA driver
    Disk space
  • 1.03GB for cellXpress only
  • Image and data file sizes are project-dependent
    Memory
  • Minimum: 4GB
  • Recommended: at least 16GB

    Operating systems
  • macOS 13 (Ventura) or above
    Processors
  • Minimum: Apple (M1) CPUs
  • Recommended: Apple (M2) CPUs or above
  • Support multi-core processors
    Graphics Processing Unit (for CSAI acceleration)
  • Not supported
    Disk space
  • 50MB for cellXpress only
  • Image and data file sizes are project-dependent
    Memory
  • Minimum: 4GB
  • Recommended: at least 16GB

    Distributions
  • 64-bit Fedora 37, Gentoo 2.13
  • 32-bit distributions are not supported
    Processors
  • Minimum: Intel (Sandy Bridge) or AMD (Bulldozer) CPUs with AVX support
  • Recommended: Intel (Skylake) or AMD (Ryzen 1000) CPUs with AVX2 support
  • Support multi-core processors
    Graphics Processing Unit (for CSAI acceleration)
  • Minimum: GeForce GTX 1050, NVIDIA TITAN X
  • Recommended: Geforce RTX 3060 or above
  • Note: installation of the latest NVIDIA video driver, CUDA toolkit 12.1 or above, and cuDNN 8.9 or above are required
    Disk space
  • 400MB for cellXpress only
  • Image and data file sizes are project-dependent
    Memory
  • Minimum: 4GB
  • Recommended: at least 16GB

Install cellXpress on Windows 10/11

  1. Download the installation file for Windows 10/11 from https://cellXpress.org and save it into a temporary location (such as Desktop).

  2. Double click on the installation file, and read the end-user license agreement. If you accept the agreement, check “I accept the agreement” and click the “Next” button to continue. Otherwise, click on “Cancel” to stop.

  3. Enter the options as prompted and click “Install” to start the installation process.

  4. Start the program from either the Windows Start Menu, or the newly created shortcut in Desktop.

  5. If this is the first time you run cellXpress, you will be prompted with the root paths configuration menu. You must enter valid paths to start the program.

  6. Download and try on the reference projects and images.

Install cellXpress on macOS 12

  1. Download the installation file for macOS 12 from https://cellXpress.org and save it into a temporary location, such as the desktop. Please note that a64 is for the newer Apple M1/2 processors, and x64 is for Intel processors.

  2. Double click on the installation file and read the end-user license agreement. If you accept the agreement, click on the “Agree” button to continue. Otherwise, click on “Disagree” and stop.

  3. Drag the cellXpress application to the Applications folder to install it.

  4. Run cellXpress from the Applications folder.

  5. If this is the first time you run cellXpress, you will be prompted with the root paths configuration menu. You must enter valid paths to start the program.

  6. Download and try on the reference projects and images.

Install cellXpress on Linux

  1. Download the installation file for Linux (Fedora or Gentoo) from https://cellXpress.org and save it into a temporary location (e.g., /home/user/temp/cellXpress-pro-XXX-YYY.sh).

  2. Make the installation file executable.

     $ cd /homes/user/temp
 $ chmod a+x cellXpress-pro-XXX-YYY.sh

  3. Run the installation file.

    Option 1. Install under the user’s home directory (e.g., /home/user/opt/cellXpress):

     $ ./cellXpress-pro-XXX-YYY.sh

    Option 2. Install under a global directory (e.g., /opt/cellXpress) with sudo permission:

     $ sudo ./cellXpress-pro-XXX-YYY.sh –-prefix=/opt/cellXpress

  4. Read the end-user license agreement. If you accept the agreement, type “Y” and “enter” to continue. Otherwise, type “N” and “enter” to stop.

  5. [Optional] To enable GPU-acceleration for CSAI, download and install NVIDIA video driver, CUDA toolkit 11.7 or above, and cuDNN 8.5 or above.

  6. Run cellXpress.

    Option 1. Installed under the user’s home directory (e.g., /home/user/opt/cellXpress):

     $ /home/user/opt/cellXpress/latest/cellXpress.sh

    Option 2. Installed under a global directory (e.g., /opt/cellXpress) with sudo permission:

     $ /opt/cellXpress/latest/cellXpress.sh

  7. If this is the first time you run cellXpress, you will be prompted with the root paths configuration menu. You must enter valid paths to start the program.

  8. Download and try on the reference projects and images.

    Setup project and image paths

    cellXpress can access projects and images saved at local or remote file systems/services. The following project or image root paths have to be configured for the local computer before cellXpress can be start.

    Path namesPurposesPermissionsExamples
    ProjectsLocation to store cellXpress projects files (including configurations, segmentations outputs, extracted features, etc)Read/WriteC:\Projects
    ImagesLocation to store image files organized in the container format. The images may have been pre-processed, such as background subtraction or cropping.ReadC:\Images
    Raw imagesLocation to raw image files organized in container format. Original image files from the microscopes or imaging systems.ReadC:\Microscope

    1. In cellXplorer, select “Options” > “Root path”.

    2. Enter root paths and click “OK” to save them.

    Download reference projects

    The following reference projects can be downloaded directly from cellXpress:

    Project nameMarker numberImaging/staining methodImage numberSize
    BEAS-2B lung cells4Immunofluorescence1403.0GB
    COVID lung tissues4PANINI2143MB
    Lung tumors (watershed or CSAI)7Multi-spectral (Vectra Polaris)101.1GB
    Tonsil tissues (watershed or CSAI)49CODEX62.3GB

    1. In cellXplorer, select “Project” > “Download a reference project”.

    2. Select the projects and click “OK”. The project file and images will be saved under the project and image storage root paths.

    3. Load and run the reference projects following the instructions on “Load an existing project” under “Create or load existing projects” in the user guide.