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software • 4 min reading time

ODEMIS: Delmic’s open-source microscopy software

Many of Delmic’s products come with ODEMIS, our open-source microscopy software for image acquisition and analysis. Here, we will highlight the advantages of the ODEMIS software, and how you can get started with it.

ODEMIS, which stands for Open Delmic Microscope Software, is microscopy software developed by Delmic. The ODEMIS acquisition software is used for controlling Delmic’s (products on) electron microscopes, while the ODEMIS viewer can be used to load experimental data for visualization, analysis, and export. ODEMIS is open-source microscopy software, meaning the source code is available for the users to study and change according to their research needs. 

General advantages of the ODEMIS software:

  • Easy and user-friendly navigating and data management
  • Full control of the hardware and the imaging algorithms to adjust to your research
  • Simple correlative imaging workflow with overlay accuracy and stage coordinates
  • Fast data acquisition with different streams

ODEMIS is mainly used for our cathodoluminescence detectors (SPARC Spectral, SPARC Compact, and JOLT) and for METEOR, the fluorescent light microscope for cryo-EM. Below, we will provide more details on the ODEMIS software per product, as well as how to get started with the software. 

ODEMIS for the SPARC Spectral

After you obtain datasets with the SPARC Spectral, ODEMIS can be easily used to analyze the datasets and to make quantitative comparisons of your data. With ODEMIS, you can explore the composition, crystal structure, defects, optical modes, resonances, and electronic band gap of your material, as well as detect trace elements or dopants.

Furthermore, your imaging workflows can be improved with tools such as automated peak fitting, cross-cutting, averaging, export functionality, and drift correction. Additionally, if the tools do not suit your needs, you can create your own analysis algorithms in the Python scripting interface. You can further process the data by exporting it to analysis software packages such as MATLAB, Python, ImageJ, Photoshop, Origin, or Excel.

ODEMIS for the SPARC Compact and JOLT

To visualize the (RGB) intensity data, ODEMIS is a powerful and easy-to-use tool. You can perform large-area mapping and stitching to create a high-resolution composite image. Additionally, you can easily overlay intensity data with SEM images. Further data processing can be done by exporting data to analysis software packages such as MATLAB, Python, ImageJ, Photoshop, Origin, or Excel.

The large area mapping and stitching capabilities of the Delmic software is phenomenal. It is nearly impossible to find the seams in the resulting high-resolution composite image.

Prof. Cameron Davidson - Department of Geology, Carleton College


You can control all fluorescent light microscopy (FLM) settings, as well as the FIB/SEM sample stage with the ODEMIS software. You can also implement your own scripts in Python to automate routine processes such as camera exposure time optimization.

Getting started with ODEMIS

  • 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+).

Installation and updates

The ODEMIS software can be installed on our GitHub repository. The ODEMIS viewer can also be installed through the link below. 

We are continuously working on improving the ODEMIS software, and therefore provide free updates. The latest ODEMIS version is v3.2.1. Below, you can find a link to update the ODEMIS viewer for Windows. For updating ODEMIS on the microscope, you can launch the software updater on the microscope computer.

Starting and stopping the software

To start the software, you can 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.
If you want to fully stop ODEMIS (GUI and back-end), which is usually unnecessary, you can type: odemis-stop.

To run the viewer, you can launch the Odemis Viewer application or type: odemis-gui --standalone.

More information

More information on the ODEMIS software, such as advanced usage and testing, can be found on our GitHub repository. Information on ODEMIS per product can also be found on our product pages.
Open source software

Download our ODEMIS viewer v3.2.1

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Rosalie Knot

Content marketeer at Delmic. She has a Master of Science in Nanobiology and is eager to learn and write about the field of life science and material science.