Data

Tools

Indexes

Applications

Experiments

Open Source Science

odemis

Open Delmic Microscope Software

https://github.com/delmic/odemis

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 48 committers (6.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.0%) to scientific vocabulary

Keywords

microscopy python
Last synced: 6 months ago · JSON representation

Repository

Open Delmic Microscope Software

Basic Info
  • Host: GitHub
  • Owner: delmic
  • License: gpl-2.0
  • Language: Python
  • Default Branch: master
  • Size: 229 MB
Statistics
  • Stars: 51
  • Watchers: 13
  • Forks: 40
  • Open Issues: 17
  • Releases: 0
Topics
microscopy python
Created over 13 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

Odemis

Odemis (Open Delmic Microscope Software) is the open-source microscopy software of Delmic B.V.. Odemis is used for controlling microscopes of Delmic and the Odemis viewer allows to load previous experimental data for visualization, analysis and export. Delmic's mission is to empower companies and researchers by helping them achieve results that can be trusted implicitly with powerful and user-friendly solutions.

Requirements

  • Linux (tested on Ubuntu 20.04, 22.04, 24.04 x86)
  • Python (v3.8+)
  • Special (forked) version of Pyro4 from Delmic

Note: the viewer part is also tested to run on Windows (10+).

For the complete list of dependencies, see the file environment.yml.

Installation

See the doc/INSTALL.txt document for the complete installation procedure.

Basic usage

Launch the "Odemis" program, or type on a terminal: odemis-start Eventually the GUI (Graphical User Interface) will appear. As an argument it can take the name of the microscope file corresponding to the back-end. Such as: odemis-start install/linux/usr/share/odemis/sim/meteor-sim.odm.yaml

It is not usually necessary, but if you want, to fully stop odemis (GUI and back-end), type: odemis-stop

To run just the viewer, you can type: odemis-gui --standalone

Advanced usage

odemisd is the command line interface to start and manage the Odemis backend. It should be started first.

Run as odemisd ..., with ... replaced by the correct arguments. For all the possible commands see: odemisd --help

For example: odemisd --daemonize --log-level=2 src/odemis/odemisd/test/optical-sim.odm.yaml

To use the command line interface use: odemis --help

To see the list of components: odemis list

For example, to turn on the forth source of the "light" component, type: odemis set-attr light power "0.0, 0.0, 0.0, 0.2"

For example, to move the Y axis of the "stage" component by 100m, type: odemis move stage y 100

License

GPLv2, see the LICENSE.txt file for the complete license.

Extending

For information on how to extend the software, see the developer documentation. It must be first compiled, with: ``` cd doc/develop/ make html

or

make latexpdf `` Then it can be opened with: firefox _build/html/index.html or evince _build/latex/odemis-develop.pdf`

Testing

To test the software, there are several unit-test classes in each directory (in their test/ sub-directory). There are also a few example microscope configuration file in the install/linux/usr/share/odemis/.

To run all the tests, you can call util/runtests.sh.

Owner

  • Name: Delmic
  • Login: delmic
  • Kind: organization
  • Location: Delft, Netherlands

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 10,064
  • Total Committers: 48
  • Avg Commits per committer: 209.667
  • Development Distribution Score (DDS): 0.403
Past Year
  • Commits: 357
  • Committers: 13
  • Avg Commits per committer: 27.462
  • Development Distribution Score (DDS): 0.524
Top Committers
Name Email Commits
Éric Piel p****l@d****m 6,008
R. de Laat l****t@d****m 1,177
Kimon Tsitsikas t****s@d****m 833
Rinze de Laat d****t@d****m 370
Philip Winkler w****r@d****m 321
Rossberger r****r@d****m 249
Thera Pals p****s@d****m 127
ktsitsikas k****s@g****m 126
Kimon k****n@k****) 77
rinze g****t@e****l 76
Bassim Lazem l****m@l****m 72
Rinze r****e@e****l 65
Anders a****s@u****a 63
Thera Pals 4****s 58
Kleijwegt k****t@d****m 41
Nandish Patel 4****l 34
VictoriaDel m****u@d****m 31
Kleijwegt K****t@d****m 30
effting e****g@d****m 28
philipwinklerdelmic 3****c 27
Guilherme Stiebler g****t@g****m 25
Nandish Patel p****l@d****m 24
Canberk Akin f****4@g****m 21
K4rishma 3****a 21
Sabrina85 s****r@g****e 20
Anders Muskens 3****s 20
Stefan Sneep s****p@d****m 18
Mahmood-B 7****B 11
sneepstefan 1****n 11
Karishma Kumar k****r@d****m 10
and 18 more...
Committer Domains (Top 20 + Academic)
delmic.com: 20 elit.nl: 3 netrom.ro: 1 ualberta.ca¨: 1 vodemis.(none): 1 delmic-desktop.(none): 1 tudelft.nl: 1 tremplin-utc.net: 1 rinzedelaat.nl: 1 gmx.de: 1 ualberta.ca: 1 kimon-delmic.(none): 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 14
  • Total pull requests: 531
  • Average time to close issues: about 4 years
  • Average time to close pull requests: 16 days
  • Total issue authors: 8
  • Total pull request authors: 10
  • Average comments per issue: 0.86
  • Average comments per pull request: 0.43
  • Merged pull requests: 385
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 6
  • Pull requests: 280
  • Average time to close issues: 9 days
  • Average time to close pull requests: 12 days
  • Issue authors: 4
  • Pull request authors: 8
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.31
  • Merged pull requests: 188
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • pieleric (6)
  • patrickcleeve2 (2)
  • effting (1)
  • thomasaarholt (1)
  • K4rishma (1)
  • tepals (1)
  • sneepstefan (1)
  • delmic (1)
Pull Request Authors
  • pieleric (231)
  • patrickcleeve2 (94)
  • nandishjpatel (65)
  • tepals (56)
  • K4rishma (45)
  • sneepstefan (18)
  • tmoerkerken (15)
  • ilyushkin (3)
  • FCanberk (3)
  • coderabbitai[bot] (1)
Top Labels
Issue Labels
DELPHI (4) bug (3) GUI (2) enhancement (2) SECOM (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 102
proxy.golang.org: github.com/delmic/odemis
  • Versions: 102
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 6.5%
Average: 6.7%
Dependent repos count: 6.9%
Last synced: 6 months ago

Dependencies

.github/workflows/unit_tests_cloud.yml actions
  • actions/checkout v2 composite
.github/workflows/self_hosted_runner.yml actions
install/windows/setup.py pypi
setup.py pypi
.github/workflows/syntax_check_cloud.yml actions
  • actions/checkout v4 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • tj-actions/changed-files v42 composite
.github/workflows/build_debian.yml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
environment.yml conda
  • cython >=0.23.5
  • decorator >=4.0.9
  • future >=0.16.0
  • h5py >=2.5.0
  • matplotlib >=1.4.3,<3.6
  • nomkl
  • numpy >=1.13.0,<=1.23
  • opencv >=3.2.0,<5.0
  • pillow >=3.2.0
  • psutil >=4.3.0
  • pycairo >=1.10.0
  • pyinstaller >=3.6
  • pylibtiff >=0.4.2
  • python 3.10.*
  • pyyaml >=3.11
  • pyzmq >=15.2.0
  • scipy >=0.19.0,<1.15
  • setuptools >=39.2.0
  • shapely >=1.7.0
  • wxpython 4.1.1