Steps for Linux System Only

  1. Install Conda. Instructions below:

  2. Install TomoNet. The download link can be found on GitHub.

    git clone <https://github.com/logicvay2010/TomoNet>

cd TomoNet/bin
chmod a+x *py

  3. Edit your .bashrc

    ############### tomoStudio related setting ##################
export PATH=YourPath2tomoNetParentFolder/TomoNet/bin:$PATH
export PYTHONPATH=YourPath2tomoNetParentFolder/:$PYTHONPATH
############### End tomoStudio setting ##################

  4. Create a new environment by typing/copying the following commands in the terminal one by one:

### First, please check that your pip version (24.x is having issue installing pytorch_lightning)
### if pip in version >= 24.x.x or some too old version, 
### please change your pip version to 23.1.2 by "pip install pip==23.1.2"

conda create -n tomonet python==3.8 (new python(3.10) version is problematic)
conda activate tomonet 
# Please use the correct cuda version
conda install pytorch==2.0.1 pytorch-cuda==11.8 -c pytorch -c nvidia

~~~~conda install cudatoolkit==11.8.0 cudnn==8.9.2.26 -y

conda install pyqt
#need pip version < 24.1
pip install numpy==1.19 pytorch_lightning==1.6.4 mrcfile scipy fire tqdm scikit-image matplotlib imodmodel psutil eulerangles starfile
  1. An alternative conda env installation, please check which one works for you.
### First, please check that your pip version (24.x is having issue installing pytorch_lightning)
### if pip in version >= 24.x.x or some too old version, 
### please change your pip version to 23.1.2 by "pip install pip==23.1.2"

# Please use the correct cuda version, 11.8 or 12.1 or others
conda create -n tomonet pytorch=2.0.1 pytorch-cuda=12.1 -c pytorch -c nvidia -y (new python(3.10) version is problematic)
conda activate tomonet 

conda install pyqt
#need pip version < 24.1
pip install numpy==1.19 pytorch_lightning==1.6.4 mrcfile scipy fire tqdm scikit-image matplotlib imodmodel psutil eulerangles starfile
  1. check installation
tomoNet.py &

Run the above line to launch TomoNet GUI

The following software needs to be installed for some of TomoNet’s modules.