Installation with Anaconda/Miniconda


This Section is still a work in progress and will only work with SmartScope >=0.62


  • Anaconda or Miniconda

  • IMOD

  • Other system dependencies:

    # For ubuntu
    sudo apt-get install default-libmysqlclient-dev build-essential libglib2.0-0 ffmpeg libsm6 libxext6

Setting up the SmartScope environment

  1. Clone or download the git repository and navigate to the directory

    git clone
    cd SmartScope
  2. Create the environment and install the python dependencies

    conda create -n smartscope python=3.9 cudatoolkit=10.2 cudnn=7.6 numpy==1.21
    conda activate smartscope
    pip install torch==1.8.2 torchvision==0.9.2 torchaudio==0.8.2 --extra-index-url
    pip install -r config/docker/requirements.txt
    pip install -e . --no-dependencies
    pip install ./SerialEM-python --no-dependencies
  3. Set up the environment variables

    1. Create your own copy of the environment template

      cp config/conda/conf-template.env conf.env
    2. Open the file in a text editor and fill up the variables to suit your system

      Click here for details about the variables.