nionswift_atom_manipulator

Single-atom manipulation tool for Nion Swift

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Prerequisites

Anaconda/Miniconda Python 3.8 environment with Nion Swift installed (see https://nionswift.readthedocs.io/en/stable/installation.html)

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Installation

1. Activate your Anaconda/Miniconda environment with Nion Swift installed (see prerequisites).

2. Install the conda packages listed below. These will not be installed in step 5 as dependencies.

   • numpy
   • scipy
   • matplotlib
   • scikit-image

3. (optional: enables element identification) Install the pip package periodictable.

4. Install the non-conda packages listed below. These will not be installed in step 5 as dependencies.

   • double_gaussian_blur (see https://github.com/arpostl/double_gaussian_blur)
   • fourier_scale_calibration (see https://github.com/jacobjma/fourier-scale-calibration)
   • nionswift_structure_recognition (see https://github.com/jacobjma/nionswift-structure-recognition)
   • nionswift_univie_tractorbeam (see [T.B.A.])
   • (optional: enables simulation mode) nionswift-usim (fork, see https://github.com/jacobjma/nionswift-usim)

5. Install this package by executing the provided setup.py. The following commands are valid if in a terminal (Linux, MacOS) or command prompt (Windows) and navigated to the root folder of this package.

$ python3 ./setup.py install

or

$ pip3 install .

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Infographics

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Screenshot of GUI

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Acknowledgements

Cordial thanks for coding and support go to

• Toma Susi (https://github.com/TomaSusi)
• Jacob Madsen (https://github.com/jacobjma)
• Andreas Mittelberger (https://github.com/Brow71189)
• Christoph Hofer (https://github.com/christophhofer40)
• Nion company (https://github.com/nion-software)