Image Processing and Analysis at BIC

As a BIC user, you have access to workstations equipped with diverse image analysis software, including both licensed and free-ware products. These tools support image processing, intensity measurements, object counting, and the creation of movies and 3D models. The workstations are conveniently situated next to the microscopes at BIC2.

collage of three images created using the image analysis software.
Nucleus and Cytoplasm segmentation using the image analyis software CellProfiler. Photo: Florian Salomons

Image analysis tools

All workstations are equipped with the vendor’s ‘lite’ versions of the acquisition software (Zeiss Zen Lite, Olympus Micro, LAS X Lite, NIS Element Viewer, IncuCyte), along with the basic analysis tools (ImageJ/Fiji, MATLAB, CellProfiler, and QuPath). Additionally, licensed software such as Imaris, Amira, AutoQuant, and NisElements is available. If you require specialized software for your analysis, it can be installed upon request.

Workstations at the BIC facility

All workstations are free to use for BIC users but need a reservation in iLab. The working stations can be accessed remotely via the VNC Viewer, ask the BIC facility staff for the access instructions. OBS! Do not turn workstations off when finished, only log out of the BIC user account.

Workstation 3 (Imaris)

WS3 features Imaris, Anaconda/Python and KNME Analytics in addition to the ‘lite’ versions of the software and basic analysis tools.

Workstation 4 (NIS Elements)

WS4 has NIS Elements (Nikon),  FluoView (Olympus) and MERSCOPE visualizer/vpt/cellpose2 (Vizgen) in addition to basic analysis tools.

Workstation 6 (Imaris, AutoQuant deconvolution)

WS6 is a top-notch workstation with Imaris full license, however without the built-in Clearview deconvolution. Instead, it has the AutoQuant deconvolution program, in addition to the ‘lite’ versions of the microscope software and basic analysis tools.

Workstation 7 (full Imaris license with Clearview deconvolution)

WS7 is a powerful analysis station with a full Imaris license including the ClearView deconvolution module. It also features MATLAB and ‘lite’ versions of the microscope system software, plus Fiji, CellProfiler, QuPath, KNME Analytics etc.

Workstation 8

WS8 is dedicated to the big datasets analysis like obtained by light sheet microscopy. It has installed Amira, Dragonfly and programming software.


Fiji is an open-source software for microscope image analysis. With Fiji, you can visualize your results, utilize custom plugins, and create your own analysis macros for automated image processing and quantification. Explore the tutorials to get started with image analysis and enhance your skills.

CellProfiler is a free software dedicated to cell image analysis. It allows you to design pipelines for automatic processing and measure the phenotypes of interest in your images. Follow online tutorials and look at examples to learn how to build your own analysis pipelines. BIC users can also request access to materials from the CellProfiler workshop held by BIC.

Imaris, a powerful 3D and 4D image analysis software, enables scientists to explore complex biological data, visualize cellular structures, track dynamic processes, and quantify features within multidimensional microscopy images. Check out the collections of tutorial videos (123) to get the most of Imaris’ capabilities.

QuPath is a free software designed for digital pathology and whole slide image analysis. It offers a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, and facilitates developing  of new algorithms to analyze complex tissue images. Check the publication,  look at tutorials and videos for a quick start.

The Microscopy Series on iBiology is a collection of free online tutorials that cover the basics of optics, transmitted light microscopy, various methods of imaging fluorescent samples, camera operation, image processing, and the latest advances in light microscopy.

MicroscopyU, created by Nikon, is an educational resource that offers comprehensive information, interactive tutorials, and timely updates on all aspects of optical microscopy, photomicrography, and digital imaging.

The Fluorescence SpectraViewer by Thermo Fisher Scientific is a tool that allows users to compare the excitation and emission parameters for many fluorophores, helping them find compatible reagents and optimal filters for their experiments.

Euro-BioImaging is a European research infrastructure that provides open access to state-of-the-art imaging technologies, training, and data services in biological and biomedical imaging for life science researchers.

BIC ImageClinics

BIC ImageClinics are regular drop-in sessions for both current BIC users and those thinking about using our services. At these sessions, you can discuss with our BIC staff various aspects of microscopy, experimental design, image analysis, presentations, and more. Welcome to drop by with your questions!