Imaris is a powerful, proprietary software suite for 3D and 4D visualization, analysis, and interpretation of microscopy data. Developed by Oxford Instruments, it is widely used in the life sciences for working with complex biological image datasets, especially those acquired from advanced microscopy techniques like confocal, two-photon, and light sheet microscopy.
ZEISS ZEN (Zeiss Efficient Navigation) is the software platform developed by ZEISS for controlling their microscopy systems and analyzing microscopy data. It comes in two main versions: ZEN Blue and ZEN Black, each designed for specific applications and types of microscopes.
Fiji (Fiji Is Just ImageJ) is a powerful distribution of ImageJ, specifically tailored for biological and scientific image analysis. It comes pre-packaged with a wide range of plugins and tools, simplifying complex workflows and making it more accessible to both beginners and advanced users. Fiji is widely used in the life sciences, particularly in microscopy and bioimage analysis.
ImageJ is a free, open-source software platform for scientific image processing and analysis, originally developed by the National Institutes of Health (NIH). It is one of the most widely used tools in the scientific community due to its versatility, extensive plugin support, and active community.
NeuroLucida is a powerful software suite developed by MBF Bioscience that is widely used in neuroscience research for the analysis and visualization of neuronal morphology. It is designed for 3D neuron reconstruction, quantification of neuronal structures, and analysis of brain circuits, among other applications.
MATLAB is a high-level programming language and interactive environment primarily used for numerical computing, data analysis, and algorithm development. It is developed by MathWorks and is widely used in academia, research, and industry for tasks ranging from simple data visualization to complex simulations, mathematical modeling, and system design.
Huygens is a software suite developed by Scientific Volume Imaging (SVI), designed for advanced microscopy image processing, analysis, and visualization. It is widely used for high-resolution 3D image reconstruction, deconvolution, and other image processing tasks, particularly in the fields of biological imaging, microscopy, and neuroscience.
Huygens Remote Manager (HRM) is a web task manager that act as an interface to PPBI’s Huygens Core Deconvolution server hosted at i3S. Please contact us to learn more about Deconvolution and how you can access and use HRM to deconvolve your fluorescence images.
Stereo Investigator is a sophisticated 3D image analysis and stereology software developed by MBF Bioscience. It is widely used in neuroscience, histology, and pathology for performing high-quality quantitative analysis of biological tissues, particularly for applications requiring three-dimensional reconstructions and stereological analysis. This tool is especially helpful for researchers working with microscopic images of brain tissue, but it can be applied to various other biological tissues as well.
MBF Biosciences Online Tutorials provide educational resources for users of MBF Biosciences’ software products, such as Stereo Investigator, Neurolucida, and Tracer.
Stereo Investigator Software Manual
(available at the MICC facility)
