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Bioimage analysis



Taking an image with a fluorescent 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 fluorescence microscopy images. This is called bioimage analysis and it allows you to quantify e.g. the intensities or sizes of objects, or to track structures in a time series.

We can assist you if you need help to create a bioimage analysis workflow geared towards your specific needs. The price for this service depends on the complexity of the problem and will be discussed on a project basis.

Commercial software

To perform image processing and analysis, you need specialized software. We provide several commercial software packages on our workstations, free of charge for our microscopy users:

Imaris - Software from Bitplane for visualization and quantification of 3D and 4D microscopy data. Used for e.g. tracking of objects over time, tracing filamentous structures, analyzing colocalization, recording movies, and visualizing 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 visualizing, 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 analyzing large quantities of images, especially those acquired using our scan^R automatic microscope 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.

Free software

Several free software packages for image processing and analysis have been developed that you can download to your own computer. We also provide these on our workstations.

ImageJ - Developed at NIH, this software works on both PC and Mac and can open most image file formats. Many plugins designed for specific image analysis problems have been developed by the ImageJ community and are freely available. We can also develop and implement plugins or macros for your specific project. The installation package called Fiji comes with many plugins already installed.

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, modeling 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.

Page Manager: CCI web manager|Last update: 1/23/2020

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