MiToBo - A Microscope Image Analysis Toolbox: v2.0

The Microscope Image Analysis Toolbox MiToBo is a Java toolbox and library of basic, intermediate and advanced image processing and analysis algorithms and tools. The toolbox for instance offers various filters (e.g., Gauss and Gabor filters, rank operators, vesselness filters), image enhancement approaches, image transformations (e.g., wavelets) and segmentation algorithms (e.g., thresholding, component labeling, active contours). In addition it ships with several advanced tools mainly dedicated to specific tasks in biomedical or biological image analysis, but not restricted to these fields. Examples are tools for DAPI stained nuclei detection, neurite segmentation, cell segmentation and tracking, particle detection, as well as PaCeQuant for pavement cell shape analysis or the CytoskeletonAnalyzer2D for quantification of cytoskeleton structural patterns. MiToBo builds upon and extends the widely used image processing application ImageJ (http://imagej.nih.gov/ij/) and seemlessly integrates into Fiji (https://imagej.net/Fiji) with its own update site. All of its operators can be run from within ImageJ/Fiji, but stand-alone usage or using MiToBo as a library for your own development is also possible. Finally, since MiToBo is based on Alida (https://alida.informatik.uni-halle.de), an advanced library for integrated development of data analysis applications, it offers a user- and programmer friendly framework for developing new image processing and analysis algorithms including automatic generation of user interfaces, an online help system, automatic process documentation, and a graphical workflow editor.The MiToBo distribution is available in two versions. The basic version (file mitobo-2.0-bin.zip) contains MiToBo with all its operators, algorithms, start scripts and documentation while the extended version (file mitobo-plugins-2.0-bin.zip) also includes ImageJ plugins for directly integrating and running MiToBo from within ImageJ