Image Processing and Analysis at BIC

We use several image analysis tools for image processing, intensity measurements, object counting, creating movies and 3D models. As a user you can get access to all these services, conveniently located just next to the microscopes.

Image from Biomedicum Imaging Core. Credit: Florian Salomons.
Image from Biomedicum Imaging Core (BIC). Credit: Florian Salomons.

General Imaging analysis tools

All workstations have the vendor’s Lite versions of the acquisition software, plus ImageJ/Fiji, MATLAB, CellProfiler, QuPath. On WS2, WS3 and WS5 there is a link to the server with remote Imaris licenses. WS4 has Amira for data processing from light-sheet microscopy.


Special Imaging Analysis tools

WS6 is a top-notch workstation and has the latest full Imaris installed and is the best option for Imaris work (vs Imaris work on the remote desktops)

WS3 is also a top-notch workstation and has the latest AutoQuant installed (X3.1.3) for deconvolution

WS4 is a workstation connected with LaVision UltraMicroscope II light sheet microscope and has Amira installed



We have several workstations with different capacities and sometimes unique software, for image processing and/or analysis (see link to detailed spec list below). They are free to use for BIC users but need a reservation.

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