Postprocessing tools for tomography data

• python3 (recommendation 3.8)
• numpy
• scipy
• scikit-image
• pymesh

• Download and install Anaconda3. Example:

wget https://repo.anaconda.com/archive/Anaconda3-2020.11-MacOSX-x86_64.sh
chmod +x Anaconda3-2020.11-MacOSX-x86_64.sh
./Anaconda3-2020.11-MacOSX-x86_64.sh
... follow instructions ...

• Set up a conda environment. Example:

conda create -n tomo python=3.8

• Install required packages to created conda environment:

conda install -n tomo numpy
conda install -n tomo scipy scikit-image

• Activate conda created conda environment and install pymesh using pip:

conda activate tomo	
pip install pymesh

• clone tomoPost to local directory

git clone https://github.com/vitst/tomoPost

Optional

• Create executable and add it to env path in .bashrc

cd /local_directory/tomoPost
mkdir bin
cd bin

• Create a file runTomo with:

#!/bin/bash
python3 /path_to/local_directory/tomoPost/runPostTomo.py "$@"

• Add it to env path in .bashrc

export PATH=/path_to/local_directory/tomoPost/bin:$PATH

• test tomoPost

runTomo -h

• Requirements

  • Fiji
  • beanshell

• Instructions that should work

  • install Fiji
  • get beanshell
  • add path to Fiji and beanshell to env variable CLASSPATH (optionaly add it to .bashrc):

   export CLASSPATH="$CLASSPATH:/path_to/bsh-2.0b4.jar:/path_to/Fiji.app/jars/*:/path_to/Fiji.app/plugins/*"