Image Analysis and Data Management
CCI provides expertise, computational infrastructure, and software to support the processing and quantitative analysis of microscopy data. On this page, you can find information about our image analysis support and consultation services, custom and full-service analysis, available computational resources and software, and how image analysis connects with data management at CCI.
CCI provides expertise, computational infrastructure, and software for processing and quantitative analysis of microscopy data. We support researchers at different levels, from access to analysis resources and expert consultation to the development and implementation of complete image analysis workflows.
Acquiring an image with a light or electron microscope is often only the first step. Depending on the research question, images may require processing such as background correction, deconvolution, registration, or 3D reconstruction. Image analysis can then be used to extract quantitative information from the data by identifying, measuring, characterizing, or tracking objects and structures of interest.
CCI supports researchers in developing appropriate and reproducible image analysis workflows that transform microscopy data into quantitative results.
Image Analysis Support
The Centre for Cellular Imaging offers different levels of image analysis support depending on the needs of your project.
Consultation and Guidance
Not sure which tools or methods are most suitable for your data? We offer consultations to help you design and implement effective image analysis workflows.
Initial Free Consultation
We offer a free initial consultation to discuss your project, imaging data, analysis needs, and research questions. Based on this discussion, we can suggest suitable tools, methods, and potential analysis workflows.
Continued Support
If you require further support, we can provide additional guidance, troubleshooting, and workflow development at an hourly rate. Please refer to the CCI service pricing for more information.
Custom Image Analysis
For projects requiring more advanced image analysis, we provide tailored solutions based on your data and research questions.
Custom Workflow Development
Based on your needs, we can design and implement tailored and reproducible image analysis workflows, using existing tools where appropriate or developing macros, scripts, and custom software for processing and analysing your data.
Full-Service Image Analysis
We can perform the complete image analysis workflow for you, including image processing, quantitative analysis, and quality control. You remain involved in key decisions throughout the process to ensure that the analysis addresses your research questions and that the resulting measurements are scientifically meaningful.
Pricing
Full-service image analysis projects typically begin with a 10-hour contract covering research, development, and iterative refinement of the analysis workflow. Additional time, if required, is charged at an hourly rate. An updated list of prices is available below
Image Analysis Infrastructure
On-site Workstations
CCI provides access to high-performance workstations equipped with a broad selection of open-source and commercial software for image processing, visualization, and analysis. These systems are suitable for working with large and complex datasets that may be difficult to analyse on standard desktop computers.
Remote Access to Image Analysis Servers
CCI also provides remote access to computational resources for processing and analysing microscopy data without needing to work on site. These resources support large datasets and computationally demanding image analysis workflows.
Available Software
Our image analysis infrastructure provides access to a broad range of open-source and commercial software for image processing, visualization, and quantitative analysis. We promote the use of open and reproducible analysis workflows whenever appropriate, while providing access to specialized commercial software when required by the application.
Open-source Software
Fiji – Open-source software for image processing and analysis that supports a wide range of microscopy file formats. Its functionality can be extended through a large collection of community-developed plugins.
CellProfiler – Open-source software for automated quantitative analysis of microscopy images. It is particularly useful for building reproducible workflows for measuring large numbers of cells or other objects.
ilastik – Open-source software that uses machine learning for interactive image classification and segmentation. It is designed to make machine-learning-based image analysis accessible without requiring programming experience.
IMOD – Open-source software for processing, modelling, visualization, and 3D reconstruction of microscopy data. It is widely used for electron tomography and serial-section electron microscopy datasets.
Python – A flexible open-source programming environment for developing custom and reproducible image analysis workflows. Common tools used at CCI include Jupyter Notebooks, napari, scikit-image, and other packages from the scientific Python and bioimage analysis ecosystems.
Commercial Software
Imaris – Software for visualization and quantitative analysis of 3D and 4D microscopy data. It supports applications such as object tracking, filament tracing, colocalization analysis, and 3D rendering.
Amira – Software for visualization, processing, and analysis of multidimensional image data from different imaging modalities, including electron microscopy, CT, MRI, and 3D microscopy.
MATLAB – A general-purpose computing environment for developing custom image processing and analysis algorithms. It can also be used to create automated workflows and graphical user interfaces.
ZEN – ZEISS software for microscope image acquisition, visualization, processing, and analysis, providing a range of tools and modules for working with microscopy images.
arivis – Software for visualization and analysis of large, multidimensional imaging datasets, particularly large 3D and 4D datasets such as those generated by light-sheet microscopy.
Data Management
CCI provides infrastructure for managing microscopy data from acquisition through processing and analysis. For information about how data flow through CCI, data transfer, OMERO, and user responsibilities, see the CCI Data Management Plan.