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tomopy-short-course

Course materials for a 90 minute interactive session for learning to reconstruct three-dimensional images from two-dimensional projections using TomoPy, the open-source Python package for tomographic data processing and image reconstruction.

https://github.com/tomopy/tomopy-short-course

Science Score: 18.0%

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Keywords

learning-resources tomography workshop-materials
Last synced: 6 months ago · JSON representation ·

Repository

Course materials for a 90 minute interactive session for learning to reconstruct three-dimensional images from two-dimensional projections using TomoPy, the open-source Python package for tomographic data processing and image reconstruction.

Basic Info
  • Host: GitHub
  • Owner: tomopy
  • License: other
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 2.14 MB
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  • Stars: 14
  • Watchers: 3
  • Forks: 7
  • Open Issues: 0
  • Releases: 0
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learning-resources tomography workshop-materials
Created over 6 years ago · Last pushed about 6 years ago
Metadata Files
Readme License Citation

README.md

TomoPy Short Course

Lead by Daniel Ching from The US Department of Energy’s Argonne National Laboratory at ICTMS 2019, Cairns, Australia

Summary

In a 90 minute interactive session, we will learn to reconstruct three-dimensional images from two-dimensional projections using TomoPy, the open-source Python package for tomographic data processing and image reconstruction. The course assumes some knowledge of x-ray computed tomography, but only minimal knowledge of computer programming. Topics covered include common steps to reconstruct x-ray computed tomography data and how to choose a reconstruction algorithm.

Materials

The short course requires internet access; all activities may be performed online using Jupyter Lab hosted on MyBinder. Alternatively, with a 64-bit computer running Windows 10, macOS, or Linux, the required Python packages may be downloaded or installed using a custom pre-built miniconda installer created in advance by the instructor.

Source-code Organization

This repository contains the source files to run the workshop.

activities/ contains a conda environment yaml listing required packages, markdown pages, ipython notebooks, and materials for each of the course activities.

solutions/ contains example scripts for the two final activities.

citations.bib contains citations for related works.

build/ contains construct.yaml which is for using the conda constructor to create a custom miniconda installer which comes with TomoPy and jupyter notebook preinstalled (no internet needed).

Anonymous Survey

If you take this short course, please take a short survey providing feedback. Thanks! https://forms.gle/NK5yhVq5yGcAvRKs6

Owner

  • Name: tomopy
  • Login: tomopy
  • Kind: organization
  • Location: United States

Citation (citations.bib) 

@article{gursoy2014tomopy,
  title={TomoPy: a framework for the analysis of synchrotron tomographic data},
  author={G{\"u}rsoy, Doga and De Carlo, Francesco and Xiao, Xianghui and Jacobsen, Chris},
  journal={Journal of synchrotron radiation},
  volume={21},
  number={5},
  pages={1188--1193},
  year={2014},
  publisher={International Union of Crystallography}
}

@article{de2014scientific,
  title={Scientific data exchange: a schema for HDF5-based storage of raw and analyzed data},
  author={De Carlo, Francesco and G{\"u}rsoy, Doga and Marone, Federica and Rivers, Mark and Parkinson, Dilworth Y and Khan, Faisal and Schwarz, Nicholas and Vine, David J and Vogt, Stefan and Gleber, S-C and others},
  journal={Journal of synchrotron radiation},
  volume={21},
  number={6},
  pages={1224--1230},
  year={2014},
  publisher={International Union of Crystallography}
}

@article{pelt2016integration,
  title={Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data},
  author={Pelt, Dani{\"e}l M and G{\"u}rsoy, Doga and Palenstijn, Willem Jan and Sijbers, Jan and De Carlo, Francesco and Batenburg, Kees Joost},
  journal={Journal of synchrotron radiation},
  volume={23},
  number={3},
  pages={842--849},
  year={2016},
  publisher={International Union of Crystallography}
}

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