TomoTools package

TomoTools is a Hyperspy-based software package for the aligment and reconstruction of electron tomography data from TEM/STEM instruments. Tools are provided for basic tilt series data processing, stack alignment, and reconstruction using the astra-toolbox.

Installation

Anaconda (Preferred):

• The required packages can be installed into an existing Anaconda environmnent. Install major dependencies Astra Toolbox and HyperSpy. Optional but highly recommended, ipympl should also be installed to enable interactive plotting in Jupyter Lab.

  NOTE: astra-toolbox must be installed first due to a dependency conflict.

  conda create -n tomo
  conda activate tomo
  conda install -c astra-toolbox astra-toolbox 
  conda install -c conda-forge hyperspy 
  conda install -c conda-forge ipympl
  conda update --all

• Install the TomoTools package from GitHub:

  pip install git+https://github.com/usnistgov/tomotools.git

Removal

The package can be removed with:

pip uninstall tomotools

Usage

In python or ipython:

import tomotools.api as tomotools
stack = tomotools.load('TiltSeries.mrc')

Documentation is very limited at this point

Documentation

Release: https://github.com/andrewherzing/tomotools

A demo notebook is available in the resources folder. More documentation will be made available over time.

Related projects

http://hyperspy.org/

https://www.astra-toolbox.com/