Odemis
ODEMIS

Software package for microscopy solutions

All DELMIC systems come with the specially developed ODEMIS software package. The ODEMIS software extends the capabilities of your microscope by closely integrating hardware with a straightforward software interface. ODEMIS is designed to be user-friendly for the easy navigation of your sample. The intuitive user interface of ODEMIS guides the user in every step of the imaging workflow.

ODEMIS is open-source and makes use of the open file formats OME-TIFF and HDF5. Other powerful tools that improve your imaging workflow include auto-focus, export functionality and a history trail that records your previous stage coordinates.

For expert users, a scripting interface in Python gives you full control of the hardware and the imaging algorithms.

For an overview of the version we are currently using and the complete change log, have a look at our Github repository.

Integrated software for SECOM

Integrated software for SECOM

Combining different types of data obtained at varying length scales makes correlative microscopy a challenging task. The software package ODEMIS greatly simplifies your correlative imaging workflow as you no longer have to be concerned with overlay accuracy and stage coordinates, leaving time to focus on imaging.

 

ODEMIS gives you control over both the fluorescence and electron microscope and navigating the sample is easy with either the fluorescence or SEM channel. The user interface is organized into different streams: one for acquiring fluorescence data, one for acquiring SEM data and two combined streams. The fluorescence stream is equipped with a fluorophore database and you can use multiple color channels with individual settings per channel.

To simplify correlative microscopy, ODEMIS features a unique fully automated alignment procedure resulting in accurate, unbiased overlays on every specimen. This overlay is directly visualized in the acquisition software, allowing you to quickly adapt your imaging conditions. (For more information about the automated overlay procedure, you can download our Automated Overlay Technical Note).


Integrated software for SPARC

ODEMIS allows for the easy acquisition and analysis of data. The software controls the scanning of the electron beam acquiring both secondary electron images and the triggering for the acquisition of spectral and angular resolved images. Spectral response data can immediately be subtracted from the datasets, showing the ‘clean’ spectrum at a glance.

Integrated software for SPARC

In particular, the software has several features for the successful and efficient acquisition of cathodoluminescence images. Firstly, it provides drift correction. Secondly, ODEMIS allows for the simultaneous acquisition of the secondary electron and spectral or angle-resolved images. Thirdly, the user can easily obtain images over an arbitrarily sized grid with an arbitrary number of pixels. Finally, the software can easily obtain a large number of angle-resolved images.

ODEMIS is also used in the process of analyzing data. The user can therefore easily visualize 3D CL data as a 2D MAP or pixel-by-pixel graph. The software also provides an advanced 2D slicer for 3D datasets with adjustable integration limits. For angle-resolved images, the software allows for immediate polar plotting. For spectral images, the software overlays the SEM and spectral images. ODEMIS also provides correction files (such as the system response function) to obtain a corrected spectrum in one go. Lastly, the software provides an automated peak fitting feature and files can be easily transferred to, for example, MATLAB for detailed analysis.

ODEMIS Viewer

If you are interested in trying out ODEMIS yourself, you can download a standalone image viewer here:

ODEMIS viewer

Download Odemis Viewer for Windows (version 2.6.1, 41.38 MB) 

Installation instructions for Linux-based systems can be found here:

installation-instructions-linux.jpg
Download Installation instructions for Linux