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Image Analysis

Image Analysis

Taking an image with a light or electron microscope and keeping it in its raw format might be sufficient for your needs. However, the appearance of such an image often benefits from image processing operations such as background subtraction, or more complex operations such as deconvolution or 3D rendering. You can even take this one step further and extract useful data from your images. This is called image processing and analysis, and it allows you to quantify or characterize objects of interest (segmentation, tracking, etc).

At the Centre for Cellular Imaging, we provide access to workstations dedicated to image analysis with a large set of commercial and open software. These workstations allow users to work on large data sets, which would otherwise be challenging to handle on their own infrastructure. Further, we also provide image analysis as a full service, where we build custom software solutions to accomplish your image analysis needs.

Image analysis services

The image analysis team at the CCI can assist you in your image analysis task by providing different services.


If you need to analyse your data but are not sure about the tools and the methods to use, we will set up a meeting with you to talk about your project and your needs. During this meeting, we will give you the keys to handle processing tasks for your images.

Custom software development

During our first meeting, if you think that you will not be able to handle the image processing or you don’t have access to the necessary equipment, we can build a custom solution for you. The purpose is to develop and implement macros or executable for you to be able to run it directly on your raw data.

In both cases, the first meeting is free of charge. The purpose is for you to present your project and discuss with us about it.

If you decide, after this meeting, to go for the custom solution, then the price for the service depends on the complexity of the project. Generally, we set up a 10-hours contract which contains state-of-arts learning process, development of the solution and meetings with you to present the software and adjust it if needed. If the project time needs to be extent, we will charge you by the hour. See the Prices for CCI service and equipment for more details.


In our workstations, both commercial and open-source software are available for image processing and analysis.

Commercial software

Imaris - Software from Bitplane for visualization and quantification of 3D and 4D microscopy data. Some application examples are: tracking of objects over time, tracing filamentous structures, analysing colocalization, recording movies, and visualising data. Examples of data processed with Imaris can be found in Bitplane's learning center

Amira - Thermo Scientific Amira Software is a 2D-5D platform for visualising, manipulating, and understanding life science research data from many image modalities, including EM, CT, MRI, 3D Microscopy, and other techniques. 

scan^R - High content screening software from Olympus for analysing large quantities of images, especially those acquired using our scan^R automated microscopy system. 

Matlab – General purpose computing environment that can be used to implement complex image analysis algorithms, and to create graphical user interfaces. A Matlab toolbox dedicated to image processing is also available. 

Zen – Image acquisition software for our Carl Zeiss microscopes that also contains several plugins for processing and analysis of acquired images.

Open software

ImageJ/FIJI - Developed at NIH, this software works on both PC and Mac and can open most file formats. Many plugins designed for specific image analysis problems have been developed by the ImageJ community and are freely available. The installation package called Fiji comes with many plugins already installed and you can build your own workflow (called macro). 

CellProfiler - A software package that enables scientists without training in image processing or programming to quantitatively measure phenotypes from thousands of fluorescence microscopy images automatically. 

Ilastik – A software tool that uses machine learning for image classification and segmentation. No previous experience in image processing is required. 

IMOD - A set of image processing, modelling and display programs used for tomographic or 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks and viewing 3D data from any orientation. 

Zen lite - With this software you can easily open the images that you have acquired with all our Carl Zeiss microscopes. The software is only compatible with PC.