Image Analysis Software and Hardware

COMPARE provides access to state-of-the-art high performance computing hardware for applying the latest methods from image analysis and machine learning research. 

We have expertise in a wide range of leading open source software tools and can provide customised solutions. Additionally, we can provide access to several commercial software applications.

Hardware for AI and high-performance computing (HPC)

In collaboration with Birmingham Environment for Academic Research (BEAR) we can provide access to three dedicated state-of-the-art compute nodes. These resources are invaluable for our researchers performing AI based research, accelerating workflows to enable breakthroughs in areas such as drug design, image segmentation and single particle tracking. Each node has four of NVIDIA’s latest A100 GPUs (40GB memory), twin Intel Ice Lake next generation CPUs and 512GB system RAM. We also have a further node with two NVIDIA’s P100 GPUs and 1TB system RAM. 


We provide access to six high-end image analysis workstations. Additionally, we have two Linux virtual machines. Booking is through Stratacore. Please complete the following form to request workstation booking rights:

COMPARE Workstations


We have expertise in the latest open-source tools for image analysis and can support various popular platforms including:

  • Fiji/ImageJ
  • QPath
  • CellProfiler
  • Ilastik
  • Icy

We can also provide programming support/advice for popular data-science languages including python, R and Matlab.

COMPARE code and software tools

Some computational tools and software produced by COMPARE research groups. Here we link to computation tools, please contact the relevant groups for further information and remember to cite the tools if they are used in publications and other outputs.

Contact: Jeremy Pike,
Code: and

Citation: Pike, J.A., Khan, A.O., Pallini, C., Thomas, S.G., Mund, M., Ries, J., Poulter, N.S. and Styles, I.B., 2020. Topological data analysis quantifies biological nano-structure from single molecule localization microscopy. Bioinformatics, 36(5), pp.1614-1621.

A R package for pointillist analysis of single molecule localization microscopy (SMLM) data. This package includes methods for persistence-based clustering (ToMATo), alongside DBSCAN, Voronoi tessellation and Ripley's K based clustering. There is also the capacity to simulate dSTORM data. Tutorials available as Binder ready Jupyter notebooks.

KNIME Analysis workflow for characterization of platelet spreading and morphology
Contact: Jeremy Pike,

Citation: Pike, J.A., Simms, V.A., Smith, C.W., Morgan, N.V., Khan, A.O., Poulter, N.S., Styles, I.B. and Thomas, S.G., 2021. An adaptable analysis workflow for characterization of platelet spreading and morphology. Platelets, 32(1), pp.54-58.

KNIME workflows for the segmentation and characterization of platelets. The workflow combines user placed markers with an ilastik pixel classifier to achieve cellular segmentation of densely packed cells. A random forest classifier in then used to classify platelets into user defined classed (e.g. spread/not-spread).

Arivis Vision4D: Your powerful scientific imaging software

“Arivis Vision4D is your modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size, highly scalable and independent of local system resources. Many modern microscope systems such as high-speed confocal, light sheet / SPIM, super-resolution, electron microscopy or X-ray instruments can produce huge amounts of imaging data. Arivis Vision4D gives you the power to handle your datasets without constraints and get your results in next to no time.”

Vision 4D is available at £10/hr or a year subscription. 

Huygens Professional: Get the most out of your images

“Huygens Professional is part of the Huygens Software Suite, and offers a complete workflow for deconvolution, restoration and analysis of microscopy images. With the included Wizards, you can restore images without being a specialist on image restoration and optical theory, yet tools like the Operation Window and Scripting/Python shell also facilitate image processing for experts.”

Huygens Professional is available at £10/hr or a year subscription.