ImSwitch
ImSwitch: Generalizing microscope control in Python - Published in JOSS (2021)
Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: joss.theoj.org -
✓Committers with academic emails
3 of 15 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.2%) to scientific vocabulary
Scientific Fields
Repository
ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.
Basic Info
- Host: GitHub
- Owner: xcasas
- License: gpl-3.0
- Default Branch: master
- Homepage: https://imswitch.readthedocs.io/
- Size: 38.2 MB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
ImSwitch
ImSwitch is a software solution in Python that aims at generalizing microscope control by using an architecture based on the model-view-presenter (MVP) to provide a solution for flexible control of multiple microscope modalities.
Statement of need
The constant development of novel microscopy methods with an increased number of dedicated hardware devices poses significant challenges to software development. ImSwitch is designed to be compatible with many different microscope modalities and customizable to the specific design of individual custom-built microscopes, all while using the same software. We would like to involve the community in further developing ImSwitch in this direction, believing that it is possible to integrate current state-of-the-art solutions into one unified software.
Installation
Option A: Standalone bundles for Windows
Windows users can download ImSwitch in standalone format from the releases page on GitHub. Further information is available there. An existing Python installation is not required.
Option B: Install using pip
ImSwitch is also published on PyPI and can be installed using pip. Python 3.7 or later is required. Additionally, certain components (the image reconstruction module and support for TIS cameras) require the software to be running on Windows, but most of the functionality is available on other operating systems as well.
To install ImSwitch from PyPI, run the following command:
pip install ImSwitch
You will then be able to start ImSwitch with this command:
imswitch
(Developers installing ImSwitch from the source repository should run pip install -r requirements-dev.txt instead, and start it using python -m imswitch)
Documentation
Further documentation is available at imswitch.readthedocs.io.
Testing
ImSwitch has automated testing through GitHub Actions, including UI and unit tests. It is also possible to manually inspect and test the software without any device since it contains mockers that are automatically initialized if the instrumentation specified in the config file is not detected.
Contributing
Read the contributing section in the documentation if you want to help us improve and further develop ImSwitch!
Owner
- Name: Xavier
- Login: xcasas
- Kind: user
- Location: Barcelona, Spain
- Company: Barcelona Supercomputing Center
- Repositories: 1
- Profile: https://github.com/xcasas
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite the article from preferred-citation."
authors:
- family-names: "Casas Moreno"
given-names: "Xavier"
orcid: "https://orcid.org/0000-0002-9583-9022"
- family-names: "Al-Kadhimi"
given-names: "Staffan"
orcid: "https://orcid.org/0000-0002-3488-6845"
- family-names: "Alvelid"
given-names: "Jonatan"
orcid: "https://orcid.org/0000-0002-3554-9322"
- family-names: "Bodén"
given-names: "Andreas"
orcid: "https://orcid.org/0000-0001-9302-7576"
- family-names: "Testa"
given-names: "Ilaria"
orcid: "https://orcid.org/0000-0003-4005-4997"
title: "ImSwitch: Generalizing microscope control in Python"
doi: "10.5281/zenodo.5196461"
url: "https://github.com/kasasxav/ImSwitch"
preferred-citation:
type: article
authors:
- family-names: "Casas Moreno"
given-names: "Xavier"
orcid: "https://orcid.org/0000-0002-9583-9022"
- family-names: "Al-Kadhimi"
given-names: "Staffan"
orcid: "https://orcid.org/0000-0002-3488-6845"
- family-names: "Alvelid"
given-names: "Jonatan"
orcid: "https://orcid.org/0000-0002-3554-9322"
- family-names: "Bodén"
given-names: "Andreas"
orcid: "https://orcid.org/0000-0001-9302-7576"
- family-names: "Testa"
given-names: "Ilaria"
orcid: "https://orcid.org/0000-0003-4005-4997"
doi: "10.21105/joss.03394"
title: "ImSwitch: Generalizing microscope control in Python"
journal: "Journal of Open Source Software"
publisher:
name: "The Open Journal"
year: 2021
volume: 6
issue: 64
start: 3394
GitHub Events
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Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| stafak | s****k@k****e | 506 |
| xaviercm94 | x****m@k****e | 209 |
| Xavier | 3****v | 176 |
| jonatanalvelid | 3****d | 147 |
| beniroquai | b****d@g****e | 103 |
| Jacopo Abramo | j****o@g****m | 30 |
| edabngl | e****4@g****m | 20 |
| xaviercm94 | 3****4 | 18 |
| Andreas Bodén | a****n@A****E | 11 |
| Dirk Boonzajer Flaes | d****s@l****e | 7 |
| Andreas Bodén | a****n@a****e | 4 |
| jhnnsrs | j****s@g****m | 2 |
| Blaise Thompson | b****e@u****m | 2 |
| Dieter Weber | d****r@f****e | 1 |
| David McFadden | 2****d | 1 |
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Dependencies
- actions/checkout v2 composite
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- pypa/gh-action-pypi-publish master composite
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- pytest >=6.2 development
- pytest-qt >=3.3 development