Java

automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

Reconstruct big images from overlapping tiled images on a Spark cluster.

The code is based on the Stitching plugin for Fiji https://github.com/fiji/Stitching

Estimate the positions and spacing between sections (or at local points) of three dimensional image data. This method may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2.

The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.