Image Analysis Resources

      Image analysis is a critical component of the microscopy workflow. To ensure you get the best possible result in your experiments analysis requirements should be defined during the experimental design phase. Factors such as sample preparation, microscope used, and sampling resolution will directly impact the feasibility of downstream analysis.

      Regarding image analysis, AIC operates primarily as a self-service facility. We provide the necessary infrastructure and software environment for researchers to perform their own analysis. Please ask our staff to see what is available.

      Analysis Workstations

      The facility maintains two high-performance workstations equipped with dedicated GPUs and high-capacity RAM to facilitate the processing of large microscopy datasets.

      Access to analysis computers requires a reservation. Please book them using OpenIris.

      Commercial Software

      The Advanced Imaging Core provides access to specialized commercial software packages on our analysis workstations. These tools are recommended for complex 3D visualization, large data handling, and specific restoration tasks.

      • Imaris (Oxford Instruments): Comprehensive software for 3D/4D visualization, surface rendering, and object tracking.
      • arivis Vision4D: specialized platform optimized for handling and rendering multi-terabyte datasets.
      • Huygens (SVI): Industry-standard software for image deconvolution and restoration, improving resolution and signal quality.

      Note: Software license availability varies by workstation. Please verify the configuration in the booking system.

        Full-Service Analysis & Custom Development

        For projects requiring extensive custom analysis, script development, or full-service data extraction, we refer users to the Turku BioImaging (TBI) Image Data Team.

        → Contact the Image Data Team

        Open-Source Software

        We actively support the use of open-source software to promote scientific reproducibility and flexibility. The following tools are widely used in the community.

        General Image Processing

        • Fiji (ImageJ) – An extensible platform for biological image analysis with a comprehensive plugin ecosystem.
        • napari – A multi-dimensional image viewer for Python, suitable for visualizing large datasets.
        • ilastik – Interactive machine learning tool for user-friendly segmentation and object classification.
        • CellProfiler – Designed for high-throughput automation and quantitative analysis of large image sets.
        • QuPath – specialized software for whole-slide image analysis and spatial phenotyping.

        Deep Learning & AI

        • Cellpose – A generalist, deep learning-based segmentation algorithm for cells and nuclei.
        • DL4MicEverywhere – A platform for training and applying deep learning models via Jupyter notebooks.

          Vendor Viewers

          To ensure accurate metadata extraction or simple visualization without instrument control, the following free vendor-specific viewers are recommended:

          Last updated on January 27, 2026