instamatic

Python program for automated electron diffraction data collection

https://github.com/instamatic-dev/instamatic

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 14 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
1 of 14 committers (7.1%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.8%) to scientific vocabulary

Keywords

3d-electron-diffraction automation data-collection electron-diffraction electron-microscopy micro-ed serial-crystallography

Keywords from Contributors

cluster-analysis xds powder-diffraction profile-refinement structure-refinement topas background-correction

Last synced: 6 months ago · JSON representation ·

Repository

Python program for automated electron diffraction data collection

Basic Info

Host: GitHub
Owner: instamatic-dev
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://instamatic.readthedocs.io/
Size: 10.1 MB

Statistics

Stars: 59
Watchers: 6
Forks: 30
Open Issues: 10
Releases: 23

Topics

3d-electron-diffraction automation data-collection electron-diffraction electron-microscopy micro-ed serial-crystallography

Created almost 9 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing Code of conduct Citation

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 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 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 for a TEM interface to control a FEI Tecnai-TEM 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.

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 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

Maintenance

2025-now: @Baharis
2015-2025: @stefsmeets

Owner

Name: Instamatic
Login: instamatic-dev
Kind: organization

Repositories: 5
Profile: https://github.com/instamatic-dev

Citation (CITATION.cff)

# YAML 1.2
---
abstract: "Python program for automated electron diffraction data collection."
authors:
  -
    affiliation: "Netherlands eScience Center"
    family-names: Smeets
    given-names: Stef
    orcid: "https://orcid.org/0000-0002-5413-9038"
  -
    affiliation: Vironova
    family-names: Wang
    given-names: Bin
    orcid: "https://orcid.org/0000-0002-4327-6424"
  -
    affiliation: "Amsterdam Scientific Instruments"
    family-names: Hogenbirk
    given-names: Erik
  -
    affiliation: "Charles University"
    family-names: Rainer
    given-names: Daniel
    orcid: "https://orcid.org/0000-0002-3272-3161"
  -
    affiliation: "Czech Academy of Sciences"
    family-names: Tchoń
    given-names: Daniel Mariusz
    orcid: "https://orcid.org/0000-0003-4798-867X"
cff-version: "1.1.0"
date-released: 2021-08-09
doi: "10.5281/zenodo.1090388"
license: "BSD-3-Clause"
message: "If you use this software, please cite it using these metadata."
title: Instamatic
version: "2.1.1"
...

GitHub Events

Total

Create event: 7
Release event: 2
Issues event: 24
Watch event: 3
Delete event: 4
Member event: 1
Issue comment event: 111
Push event: 32
Pull request review comment event: 91
Pull request review event: 87
Pull request event: 47
Fork event: 6

Last Year

Create event: 7
Release event: 2
Issues event: 24
Watch event: 3
Delete event: 4
Member event: 1
Issue comment event: 111
Push event: 32
Pull request review comment event: 91
Pull request review event: 87
Pull request event: 47
Fork event: 6

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 1,344
Total Committers: 14
Avg Commits per committer: 96.0
Development Distribution Score (DDS): 0.569

Top Committers

Name	Email	Commits
Stef Smeets	s**s@m**e	579
Stef Smeets	s**s@t**l	569
Bin Wang	w**7@s**m	73
Stef Smeets	s**s@u**m	53
Stef Smeets	s**s@e**l	36
binwang	b**g@v**m	18
ErikHogenbirk	e**k@a**m	6
Daniel N. Rainer	d**r@o**m	2
Jonas Ångström	j**7@w**e	2
Thomas Aarholt	t**t@g**m	2
TM	t**g@g**m	1
BinWang	b**g@s**e	1
Kotaro Tanaka	4**9@u**m	1
Paul van Schayck	p**e@g**m	1

Committer Domains (Top 20 + Academic)

sas.se: 1 win.su.se: 1 amscins.com: 1 vironova.com: 1 esciencecenter.nl: 1 sina.com: 1 tudelft.nl: 1 mmk.su.se: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 53
Total pull requests: 98
Average time to close issues: 3 months
Average time to close pull requests: 7 days
Total issue authors: 16
Total pull request authors: 14
Average comments per issue: 2.94
Average comments per pull request: 1.28
Merged pull requests: 82
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 19
Pull requests: 43
Average time to close issues: about 1 month
Average time to close pull requests: 5 days
Issue authors: 6
Pull request authors: 4
Average comments per issue: 1.95
Average comments per pull request: 2.16
Merged pull requests: 34
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

stefsmeets (11)
thomasaarholt (8)
kttn8769 (5)
iverks (5)
Baharis (4)
viljarjf (4)
GearoidM (3)
rds-itga (3)
Binary-Vanguard-12138 (2)
Taimin (1)
CSSFrancis (1)
dkajfnln (1)
magnunor (1)
aurorateien (1)
komoto48g (1)

Pull Request Authors

stefsmeets (36)
Baharis (29)
asdfdsa (15)
viljarjf (8)
Binary-Vanguard-12138 (4)
iverks (4)
Junschen1 (2)
Taimin (2)
thomasaarholt (2)
kttn8769 (1)
danielnrainer (1)
dependabot[bot] (1)
PaulVanSchayck (1)
jonasangstrom (1)

Top Labels

Issue Labels

enhancement (1)

Pull Request Labels

enhancement (10) bug (7) dependencies (3)

Packages

Total packages: 1
Total downloads:
- pypi 147 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 17
Total maintainers: 2

pypi.org: instamatic

Python program for automated electron diffraction data collection

Documentation: https://instamatic.readthedocs.io/
License: BSD License
Latest release: 2.1.1
published 10 months ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 147 Last month

Rankings

Dependent packages count: 10.1%

Dependent repos count: 21.6%

Average: 23.8%

Downloads: 39.8%

Maintainers (2)

baharis stefsmeets

Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi

autodocsumm *
ipython *
matplotlib *
nbsphinx *
nbsphinx-link *
numpy *
pandas *
pyyaml *
readthedocs-sphinx-search *
scikit-image *
scikit-learn *
scipy *
sphinx *
sphinx_rtd_theme *
tqdm *

pyproject.toml pypi

check-manifest * develop
pre-commit * develop
pytest >=5.4.1 develop
pytest-cov >=2.8.1 develop
comtypes >=1.1.7
h5py >=2.10.0
ipython >=7.11.1
lmfit >=1.0.0
matplotlib >=3.1.2
mrcfile >=1.1.2
numpy >=1.17.3
pandas >=1.0.0
pillow >=7.0.0
pyserialem >=0.3.2
python >=3.7.0
pywinauto >=0.6.8
pyyaml >=5.3
scikit-image >=0.17.1
scipy >=1.3.2
tifffile >=2019.7.26.2
tqdm >=4.41.1
virtualbox >=2.0.0

requirements.txt pypi

check-manifest *
comtypes >=1.1.7
h5py >=2.10.0
ipython >=7.11.1
lmfit >=1.0.0
matplotlib >=3.1.2
mrcfile >=1.1.2
numpy >=1.17.3
pandas >=0.25.3
pillow >=7.0.0
pre-commit *
pywinauto >=0.6.8
pyyaml >=5.3
scikit-image >=0.16.2
scipy >=1.3.2
tifffile >=2019.7.26.2
tqdm >=4.41.1
virtualbox >=2.0.0

.github/workflows/publish.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/test.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite

environment.yml pypi

instamatic

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

readme.md

Instamatic

Installation

OS requirement

Package dependencies

Documentation

Reference

Maintenance

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: instamatic

Rankings

Maintainers (2)

Dependencies