Steps for Linux System Only

1. Install Conda. Instructions below:

   • Conda is used to build an isolated environment for specific programs to avoid software conflicts.

     https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

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 
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
pip install numpy==1.19 pytorch_lightning==1.6.4 mrcfile scipy fire tqdm scikit-image matplotlib imodmodel psutil eulerangles starfile

tomoNet.py &

Run the above line to launch TomoNet GUI

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

• MotionCorr2 for Motion correction
• CTFFIND4 for CTF estimation
• Imod for basic operations on MRC files, visualization, and manual picking (REQUIRED)
• AreTomo for fiducial less Automatic tomography reconstruction
• PEET 1.15 for particle picking (REQUIRED for lattice particle picking)
• IsoNet for tomogram denoising and missing-wedge compensation
• ChimeraX for sub-tomogram place back

You do not have to install all of them if you do not need to use the specific function.