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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 18.04 and 20.04 x86)
  • Python (v3.6+)
  • 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 requirements.txt.

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.

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-cli --help

To see the list of components: odemis-cli --list

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

For example, to move the Y axis of the "stage" component by 100µm, type: odemis-cli --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.