Local Install


For the main required Python packages (numpy, scipy, etc.) we recommend using Anaconda for Python 3.6

ANTs & Convert3D (c3d)

If either ANTs or c3d are not installed on your machine, run install_depends.sh, located in the project directory. The required software will be installed in the depends directory. If you are intrested to install c3d on MacOS or Windows, you can dowanlod it from this link.

Installing package and dependencies for iCVMapp3r locally

  1. Clone repository

     git clone https://github.com/AICONSlab/iCVMapp3r.git iCVMapp3r
     (or install zip file and uncompress)
     cd iCVMapp3r

    If you want to create a virtual environment where iCVMapp3r can be run,

     conda create -n icvmapper python=3.6 anaconda
     conda activate icvmapper

    To end the session,

     conda deactivate

    To remove the environment

     conda env remove --name icvmapper
  2. Install dependencies

     pip install git+https://www.github.com/keras-team/keras-contrib.git

    If the computer you are using has a GPU:

     pip install -e .[icvmapper_gpu]

    If not:

     pip install -e .[icvmapper]
  3. Test the installation by running

     icvmapper --help

    To confirm that the command line function works, and


    To launch the interactive GUI.

Download deep models

Download the models from this link and place them in the “models” directory

For tab completion

pip3 install argcomplete

Updating iCVMapp3r

To update iCVMapp3r, navigate to the directory where iCVMapp3r was cloned and run

git pull
pip install -e .[{option}] -process-dependency-links

where “option” is dependent on whether or not you have a GPU (see package installation steps above)