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
- 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.
A DigitalMicrograph script for collecting cRED data on a OneView camera (or any Gatan camera) can be found in the dmscript directory.
If you find this software useful, please consider citing one of the references below and/or refer to the source code in your publications:
- S. Smeets, B. Wang, M.O. Cichocka, J. Ångström, and W. Wan, (2018, December 7). Instamatic (Version 1.0.0). Zenodo. http://doi.org/10.5281/zenodo.2026774
Some of the methods implemented in Instamatic are described in:
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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,
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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
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
Use pydoc to access the full API reference: pydoc -b instamatic
- Python3.6
- comtypes
- lmfit
- matplotlib
- numpy
- pandas
- Pillow
- scipy
- scikit-image
- tqdm
- pyyaml
- h5py
- IPython
Requirements can be installed via:
pip install -r requirements.txt
The simplest way is to 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.
Alternatively, the latest development version can always be obtained via:
https://github.com/stefsmeets/instamatic/archive/master.zip
To install:
pip install -r requirements.txt
python setup.py install