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.
| Category | Name | Version | Availability | Description |
|---|---|---|---|---|
| Multifunctional viewer |  Fiji | 2.14/1.54f | All workstations | FIJI (Fiji Is Just ImageJ) is an image processing package that includes the ImageJ image analysis software and a massive library of its plugins suitable for a wide range of applications in image pre-processing, analysis, statistics and data visualisation. It is free, open source, scriptable in multiple programming languages, and supports all file formats used in scientific imaging. It also has a thriving community of users, willing to provide support and share pre-built scripts on forums (e.g. www.forum.image.sc). |
| Multifunctional viewer |  Imaris | 9.9.1 | All workstations 8 x floating licenses Booking required | Visualization and analysis software with interactive 3D viewer. It is suitable for image pre-processing, intensity-based object detection, statistical analysis and creation of interactive lineage trees. Promotes workflow automation with guided batch job setup and has a two-way interface for customization in Matlab, Java or Python as well as bridge to/from Fiji. Additional functionality can be added with official and community-developed plugins. |
| Multifunctional viewer |  Arivis | 4.0.0 | All workstations 1 x floating licenses Booking required | Multifunctional software for visualisation and handling of big image data in 2D, 3D and 4D. It uses state-of-the-art algorithms for multimodal data fusion, deep learning based segmentation and statistical analysis. It supports plugins, scripts and has a user friendly interface. Utilizes GPU acceleration which further improves performance with large datasets. |
| Multifunctional viewer |  Napari | 0.4.17 | VDI, ML-VDI | Python-based viewer for visualisation, annotation and analysis of large multidimensional images. It is open source and supports plugins. Python integration allows for the advanced workflow automation with custom scripts that leverage the power of data analysis libraries (e.g. NumPy, SciPy, scikit-image). |
| Segmentation |  CellPose | 2.0 | All workstations | Deep learning based segmentation algorithm. Includes a set of pre-trained high quality segmentation models for a variety of applications. Also supports manual model creation, but it takes more time and requires more precision than alternative solutions and can only be done on 2D datasets. Available as a standalone application, a Python library and as a plugin for ImageJ and QuPath. |
| Segmentation |  Ilastik | 1.4 | All workstations | A simple, user-friendly tool for interactive machine learning based image classification, segmentation and analysis. Available as a standalone software, Python library and as a plugin for Fiji and QuPath. |
| Deconvolution |  Huygens Professional | 22.10 & 23.4 | All workstations 2 x floating licenses Booking required | Software package that offers a complete workflow for deconvolution, restoration 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. |
| Histopathology |  QuPath | 0.4.1 | All PCs, VDI | Software solution for quantitative histopathology. It allows visualisation and analysis of large 2D slide scanner datasets. Includes tools for manual annotation, machine learning based tissue classification and deep learning based cell segmentation. The functionality of the program is extensible using Java based plugins and scriptable using the Groovy programming language. |
| Tracking |  SLEAP | 1.2.9 | ML-VDI | Deep learning based software for animal pose tracking. It can track any type or number of animals, which is most relevant for neuroscience and behavioural studies. Includes a user-friendly labeling interface for active training and proofreading. |
| Tracking |  DeepLabCut | 2.3.5 | ML-VDI | Deep learning based software for animal and object tracking. Supports simultaneous tracking of multiple objects and comes with a community-sourced model zoo trained on a variety of animals and scenarios. It also allows for a flexible model creation with a high degree of precision. |
| SMLM | Huygens Localizer | 22.10 & 23.4 | All workstations 2 x floating licenses Booking required | Software for Single Molecule Localisation Microscopy (SMLM) image analysis. Allows processing of images acquired with technologies such as Photoactivated Localisation Microscopy (PALM), Stochastic Optical Reconstruction Microscopy (STORM), Ground State Depletion (GSD), and DNA PAINT. It has a user-friendly interface and broad compatibility with various microscopy file formats. |
| SMLM | RapidStorm | 3.3.1 | VDI, ML-VDI | Image analysis software for single molecule localisation microscopy (SMLM). It is suitable for both beginners and advanced users and provides an extensive list of parameters for customisation. |
| 3D Graphics |  Blender | 3.5.0 | PC 07, ML-VDI | Software for 3D model rendering, editing and animation. Supports data import from scientific image analysis applications (e.g. Imaris, Fiji, Arivis). |