Introduction to Turku BioImaging key technologies (see the Turku BioImaging Black Book for more information).

Image Analysis

Whatever the imaging method used, image acquisition is only the beginning of the project. Processing, visualizing, and quantitatively analyzing image data is crucial in generating meaningful results. Turku BioImaging offers unique assistance in this area, thanks to in-house software production.

In collaboration with the University of Jyväskylä, and other partners, a large open-source software package termed BioImageXD has been created, for post-processing of multidimensional biomedical image data. Acquired images are simply opened in BioImageXD, which can directly read common microscopy file formats and import regular image files. Hundreds of tools are available, ranging from basic processing such as noise removal and contrast adjustment to advanced tools including segmentation, and quantitative and statistical analyses. Command pipelines can easily be created and saved, and for high content analysis hundreds of files can be processed in a single session. BioImageXD also creates three-dimensional views and four-dimensional movies.

The feature set of BioImageXD is one of the most versatile available. The software can be used to analyze individual image pixels, to explore co-localization or to make intensity measurements within regions of interest. Structures such as cells or organelles can be extracted from an image using any of numerous segmentation methods, and parameters such as size, shape, distribution, and amount, can be quantified. The movements of cells or other objects such as intracellular vesicles can be tracked. The software can also perform bleaching and focus drift compensation, deconvolution, and automatic background removal to enhance image quality. Images can be interactively visualized in three dimensions, and distances (for example) can be measured. High-quality images and videos can be created for presentations and publications.

The BioImageXD software is freely available for download at, and user support is available through