Installation with Anaconda/Miniconda

Warning

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

Requirements

• 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 https://github.com/NIEHS/SmartScope.git
   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 https://download.pytorch.org/whl/lts/1.8/cu102
   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.