University of Jyväskylä, University of Turku and Max Planck Institute


Measured variables surface, length, width, volume, 3D-reconstruction, color
Operating system windows, mac, linux
Licence open-source, freeware
Automation level automated, semi-automated, manual
Plant requirements any
Export formats xls, csv, txt
Other information -

Scientific article(s)

BioImageXD: an open, general-purpose and high-throughput image-processing platform
Pasi Kankaanpää, Lassi Paavolainen, Silja Tiitta, Mikko Karjalainen, Joacim Päivärinne, Jonna Nieminen, Varpu Marjomäki, Jyrki Heino, Daniel J White
Nature Methods, 2012 View paper

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BioImageXD is a multi-purpose post-processing tool for bioimaging. The software can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once. Animations of 3D renderings can be easily created using virtual camera flying paths or key-frames. Image processing tools include deconvolution, registration and tens of tools for mathematical and logical processing and noise reduction. Analysis tools cover both object-based and voxel-based approaches, with for instance versatile tools for colocalization analysis, numerous segmentation methods with elaborate numerical analyses, and an advanced motion tracking algorithm. All processing and analysis methods can be built into pipelines and run for hundreds of datasets at once with the Batch Processor, and simulated image data can be created for method validation. BioImageXD features an intuitive graphical user interface, designed to enable accurate scientific quality and control, and image processing in high throughput.


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