Image analysis software

The Imaging and Optics Facility provides various types of software for analysis of data acquired on our systems. We aim to keep all the software up to date and in line with current trends in image analysis.

If you need assistance with any software, refer to our FAQ or get into contact with us.

If you require Software that is not currently available, get into contact with us.

CategoryNameVersionAvailabilityDescription
Multifunctional viewer
Fiji		2.16/1.54pAll workstationsFIJI (Fiji Is Just ImageJ): a powerful, open-source image processing package built on ImageJ and designed for scientific image analysis.
We support use of fiji on our infrastructure with
  • A host of supported and updated extensions
  • Snippets with regular highly used macros in fiji
  • Help with your pipelines
  • Sharing resources from forums such as ImageSc
Multifunctional viewer
Imaris		9.9.1 (VDI)
/11.0.1 (WS)		4x Imaris 11 (WS only)

4x Imaris 9.9 (VDI only)

Booking required		Imaris: Visualization and analysis software with interactive 3D viewer. Imaris 9.9/11.0 is suitable for:
  • Image pre-processing
  • Intensity-based object detection
  • Statistical analysis
  • Creation of interactive lineage trees
Imaris 11.0 additionally is ideal for:
  • Workflow automation with guided batch job setup
  • ML surface generating or filament workflows
Imaris also supports customization in Matlab, Java or Python as well as bridge to/from Fiji with official and community-developed plugins.
Multifunctional viewer
Arivis		4.2.2All workstations
1 x floating licenses
Booking required		Arivis Pro: Advanced software for multidimensional (2D/3D/4D) image visualization and analysis.
  • Supports end-to-end workflows from image import to analysis and visualization
  • Handles massive microscopy and imaging datasets using GPU-accelerated 3D rendering
  • Integrates AI-driven segmentation, feature extraction, and statistical analysis
  • Flexible pipeline creation with customizable operators and scripting options
Converter

Sis Converter		4.1All workstationsConverter for various file formats to add images to Arrivis Pro.
Multifunctional viewer
Napari		0.7.0All workstationsNapari: Python-based viewer for
  • Visualisation
  • Annotation
  • Analysis of large multidimensional images
  • Python integration for advanced workflows leveraging data analysis libraries like numPy, pandas
  • open source
Multifunctional viewer
QuPath		0.6.1All PCs, VDIQupath: Software solution that allows for
  • quantitative histopathology
  • visualisation
  • analysis of large 2D datasets
  • Includes tools for manual annotation
  • machine learning based tissue classification
  • deep learning based cell segmentation
  • scriptable using the Groovy programming language
Multifunctional viewer

Abberior Lightbox		2025.10.22550-gb362013e1e-win64All workstationsAbberior LiGHTBOX: Intuitive microscope control and image acquisition software for abberior MIRAVA POLYSCOPE and FACILITY systems, supporting a complete workflow for
  • confocal, STED and MINFLUX imaging setup
  • tiled scans, ROI-based acquisition and 3D image rendering
  • image post-processing and analysis pipelines
  • MINFLUX analysis
Multifunctional viewer

Zen		3.12All WorkstationsZEISS ZEN: Microscopy software suite for ZEISS imaging systems that provides a complete workflow for
  • Native support for czi files and post processing various images obtained from zeiss microscopes
  • 2D, 3D, time-lapse and multichannel image visualization
  • image processing, analysis, measurement and data management
Multifunctional viewer

NIS viewer		5.22.00All workstationsNikon NIS-Elements: Microscopy imaging software platform for Nikon microscopes and supported third-party components, offering a complete workflow for
  • Native support for nd2 files
  • 2D, 3D, time-lapse and multidimensional image visualization and analysis
  • AI-assisted processing, denoising, segmentation and deconvolution
Segmentation
CellPose		3.1.1.3 (cellpose3) / 4.1.1 (cellpose4)All workstationsCellpose: Deep learning based anatomical segmentation algorithm.
  • Includes a set of pre-trained high quality segmentation models
  • Supports manual model creation
  • Natively 2D
  • Expanded to 3D datasets with native and package support
  • A standalone application as python library
  • Plugin for ImageJ and QuPath
Segmentation
Ilastik		1.4All workstationsIlastik: Simple, user-friendly tool available in a standalone software and as a plugin for Fiji and QuPath. Suitable for interactive machine learning based
  • Image classification with multiple workflows
  • Segmentation with support for various file types
  • Analysis and advanced pieplines to detect and classify objects and pixels
Deconvolution
Huygens Professional		22.10 & 23.4All workstations
2 x floating licenses
Booking required		Huygens: Software package that offers a complete workflow for
  • deconvolution
  • restoration
  • Stitching and analysis of microscopy images in 2D and 3D. Also suitable for chromatic aberration correction, object tracking and colocalisation analysis. Includes a built-in "Workflow Processor" for easy batch job setup and scripting.
Tracking
SLEAP		1.2.9WS, VDI, & ML-VDISleap: Deep learning based software for
  • animal pose tracking
  • type or number of animals
  • user-friendly labeling interface
  • active training and proofreading
Programming

Miniforge		25.7.0All workstationsMiniforge: Minimal conda-forge installer for
  • installing and managing packages with conda and mamba
  • creating isolated software environments
  • accessing packages from the conda-forge channel by default
Programming

Matlab		2022WS onlyMATLAB: Programming and numeric computing environment for engineers and scientists that supports a complete workflow for
  • algorithm development and modeling
  • data analysis and visualization
  • simulation, app building and scientific computing
  • Includes a high-level language, interactive apps, specialized toolboxes, and integrations for model-based design and simulation.
Programming

Pixi		0.69.0All WorkstationsPixi: Fast, modern and reproducible package management and workflow tool for
  • creating isolated development environments
  • managing dependencies across multiple languages and platforms
  • running project tasks and workflows with built-in lock files

Programming


VS code		1.113.0All WorkstationsVisual Studio Code: Lightweight, extensible code editor and development environment suitable for image analysis workflows, offering support for
  • Support for scientific programming languages
  • interactive notebooks, scripting and debugging for image processing pipelines
  • extension-based integration with tools such as Jupyter, Git, Language linters and remote computing environments