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):
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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
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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.