MSantucci/instamatic

Python program for automated electron diffraction data collection

Instamatic

Instamatic is a Python program that is being developed with the aim to automate the collection of electron diffraction data. At the core is a Python library for transmission electron microscope experimental control with bindings for the JEOL/FEI microscopes and interfaces to the gatan/timepix/tvips cameras. Routines have been implemented for collecting serial electron diffraction (serialED), continuous rotation electron diffraction (cRED), and stepwise rotation electron diffraction (RED) data.

Instamatic is distributed as a portable stand-alone installation that includes all the needed libraries from: https://github.com/stefsmeets/instamatic/releases. However, the most up-to-date version of the code (including bugs!) is available from this repository.

Electron microscopes supported:

• JEOL microscopes with the TEMCOM library
• FEI microscopes via the scripting interface

Cameras supported:

• ASI Timepix (including live-view GUI)
• Gatan cameras through DM plugin [1]
• TVIPS cameras through EMMENU4 API

Instamatic has been extensively tested on a JEOL-2100 with a Timepix camera, and is currently being developed on a JEOL-1400 and JEOL-3200 with TVIPS cameras (XF416/F416).

[1]: A DigitalMicrograph script for collecting cRED data on a OneView camera (or any other Gatan camera) can be found at dmscript.

Installation

pip install instamatic

Alternatively, download the portable installation with all libraries/dependencies included: https://github.com/stefsmeets/instamatic/releases/latest. Extract the archive, and open a terminal by double-clicking start_Cmder.exe.

Documentation

See the documentation for how to set up and use Instamatic.

• TEMController
• Config
• Reading and writing image data
• Setting up instamatic
• Programs included
• GUI and Module system
• TVIPS module

Use pydoc to access the full API reference: pydoc -b instamatic

Reference

If you found Instamatic useful, please consider citing it or one of the references below.

Each software release is archived on Zenodo, which provides a DOI for the project and each release. The project DOI 10.5281/zenodo.1090388 will always resolve to the latest archive, which contains all the information needed to cite the release.

Alternatively, some of the methods implemented in Instamatic are described in:

• B. Wang, X. Zou, and S. Smeets, Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination, IUCrJ (2019). 6, 854-867

• B. Wang, Development of rotation electron diffraction as a fully automated and accurate method for structure determination. PhD thesis (2019), Dept. of Materials and Environmental Chemistry (MMK), Stockholm University

• M.O. Cichocka, J. Ångström, B. Wang, X. Zou, and S. Smeets, High-throughput continuous rotation electron diffraction data acquisition via software automation, J. Appl. Cryst. (2018). 51, 1652–1661

• S. Smeets, X. Zou, and W. Wan, Serial electron crystallography for structure determination and phase analysis of nanocrystalline materials, J. Appl. Cryst. (2018). 51, 1262–1273

Source Code Structure

• demos/ - Jupyter demo notebooks
• docs/ - Documentation
• instamatic/
  • TEMController/ - Microscope interaction code
  • calibrate/ - Tools for calibration
  • camera/ - Camera interaction code
  • config/ - Configuration management
  • experiments/ - Specific data collection routines
  • formats/ - Image formats and other IO
  • gui/ - GUI code
  • neural_network/ - Crystal quality prediction
  • processing/ - Data processing tools
  • server/ - Manages interprocess/network communication
  • utils/ - Helpful utilities
  • acquire_at_items.py - Stage movement/data acquisition engine
  • admin.py - Check for administrator
  • banner.py - Appropriately annoying thank you message
  • browser.py - Montage browsing class
  • exceptions.py - Internal exceptions
  • goniotool.py - Goniotool (JEOL) interaction code
  • gridmontage.py - Grid montage data collection code
  • image_utils.py - Image transformation routines
  • imreg.py - Image registration (cross correlation)
  • io.py - Some io-related scripts
  • main.py - Main entry point
  • montage.py - Image stitching
  • navigation.py - Optimize navigation paths
  • tools.py - Collection of functions used throughout the code
• scripts/ - Helpful scripts
• pyproject.toml - Dependency/build system declaration (poetry)
• setup.py - Old-style build script