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 as a portable stand-alone installation that includes all the needed libraries from: 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

• Gatan cameras through DM plugin [1]

• TVIPS cameras through EMMENU4 API

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

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

Installation

If you use conda, create a new environment:

conda create -n instamatic python=3.7
conda activate instamatic

Install using pip, works with python versions 3.7 and 3.8:

pip install instamatic

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

Installation should take less than 1 minute on a normal desktop.

Find the latest releases for the versions that have been tested on.

OS requirement

The package requires Windows 7 or higher. It has been mainly developed and tested under windows 7 and windows 10.

Package dependencies

Check pyproject.toml for the full dependency list and versions.

Documentation

See the documentation 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, 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

Getting started

Getting Started

• Setting up Instamatic
  • JEOL
  • FEI
  • Development version
  • Setting up the config files
  • Other directories
• Configuration
  • settings.yaml
  • defaults.yaml
  • calibration.yaml
  • camera.yaml:
  • microscope.yaml
• Formats
• GUI and module system
  • Usage
  • Data i/o
  • Console
  • SerialED data collection
  • cRED data collection
  • RED data collection
  • Machine learning
  • Control
  • Advanced
  • About
• Programs and scripts
  • instamatic
  • instamatic.controller
  • instamatic.serialed
  • instamatic.camera
  • instamatic.calibrate_stage_lowmag
  • instamatic.calibrate_stage_mag1
  • instamatic.calibrate_beamshift
  • instamatic.calibrate_directbeam
  • instamatic.calibrate_stagematrix
  • instamatic.flatfield
  • instamatic.stretch_correction
  • instamatic.browser
  • instamatic.viewer
  • instamatic.defocus_helper
  • instamatic.find_crystals
  • instamatic.find_crystals_ilastik
  • instamatic.learn
  • instamatic.temserver
  • instamatic.camserver
  • instamatic.dialsserver
  • instamatic.VMserver
  • instamatic.xdsserver
  • instamatic.temserver_fei
  • instamatic.goniotoolserver
  • instamatic.autoconfig
  • instamatic.install
• TEMController
  • Getting started
• cRED data collection with TVIPS
  • 1. Console window
  • 2. Input/output
  • 3. Experimental parameters
  • 4. Start/stop the experiment
  • 5. Start serial acquisition
  • 6. Other controls

Examples

Examples

• Instamatic - basic data collection
• Instamatic - grid montage
• Instamatic - montaging

API Reference

API reference

• instamatic
  • instamatic.TEMController
  • instamatic.calibrate
  • instamatic.camera
  • instamatic.config
  • instamatic.experiments
  • instamatic.formats
  • instamatic.gui
  • instamatic.neural_network
  • instamatic.processing
  • instamatic.server
  • instamatic.utils
  • instamatic.acquire_at_items
  • instamatic.admin
  • instamatic.banner
  • instamatic.browser
  • instamatic.exceptions
  • instamatic.goniotool
  • instamatic.gridmontage
  • instamatic.image_utils
  • instamatic.imreg
  • instamatic.io
  • instamatic.main
  • instamatic.montage
  • instamatic.tools

Links

Links

• 🔗 Source code
• 🔗 Issues

Indices and tables

• Index

• Module Index

• Search Page