instamatic 2.2.1
Python program for automated electron diffraction data collection
License: BSD License
Requires Python: >=3.9
Keywords: electron-crystallography, electron-microscopy, electron-diffraction, serial-crystallography, 3D-electron-diffraction, micro-ed, data-collection, automation

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# 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 ASI/TVIPS/Gatan cameras. Routines have been implemented for collecting serial electron diffraction (serialED), continuous rotation electron diffraction (cRED, aka 3D-ED / microED), and stepwise rotation electron diffraction (RED) data. For streaming cameras, instamatic includes a live-view GUI.

Instamatic is distributed via [pypi](https://pypi.org/project/instamatic) and https://github.com/instamatic-dev/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
- ASI CheeTah through `serval-toolkit` library
- TVIPS cameras through EMMENU4 API
- Quantum Detectors MerlinEM
- Gatan cameras through FEI scripting interface
- (Gatan cameras through DM plugin [1])

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

See [instamatic-dev/instamatic-tecnai-server](https://github.com/instamatic-dev/instamatic-tecnai-server) for a TEM interface to control a FEI Tecnai or FEI Titan TEM and associated cameras on Windows XP/Python 3.4 via instamatic.

[1]: Support for Gatan cameras is somewhat underdeveloped. As an alternative, a DigitalMicrograph script for collecting cRED data on a OneView camera (or any other Gatan camera) can be found [here](https://github.com/instamatic-dev/InsteaDMatic).

## Installation

If you use conda, create a new environment:

```
conda create -n instamatic python=3.11
conda activate instamatic
```

Install using pip, works with python versions 3.9 or newer:

```bash
pip install instamatic
```

## OS requirement

The package requires Windows 7 or higher. It has been mainly developed and tested under Windows 7 and higher.

## Package dependencies

Check [pypoject.toml](pypoject.toml) for the full dependency list and versions.

## Documentation

See [the documentation](https://instamatic.readthedocs.io) for how to set up and use Instamatic.

## Reference

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

Each software release is archived on [Zenodo](https://zenodo.org), which provides a DOI for the project and each release. The project DOI [10.5281/zenodo.1090388](https://doi.org/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](https://doi.org/10.1107/S2052252519007681), IUCrJ (2019). 6, 854-867

- B. Wang, [Development of rotation electron diffraction as a fully automated and accurate method for structure determination](http://www.diva-portal.org/smash/record.jsf?pid=diva2:1306254). 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](http://dx.doi.org/10.1107/S1600576718015145), 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](http://dx.doi.org/10.1107/S1600576718009500), J. Appl. Cryst. (2018). 51, 1262–1273

## Maintenance

- 2025-now: [@Baharis](https://github.com/Baharis)
- 2015-2025: [@stefsmeets](https://github.com/stefsmeets)