What is MiToBo?
The Microscope Image Analysis Toolbox MiToBo is a toolbox with a large collection of basic and advanced functions and algorithms for processing and analyzing digital images. Many tools in MiToBo target at the analysis of various kinds of microscopy data, however, most of the functionality within MiToBo is generic (see page of features for an overview). MiToBo is implemented as extension for the widely used image processing application ImageJ/Fiji and its new release ImageJ 2.0. All functions, operators and plugins of MiToBo are ready to be directly used as plugins in ImageJ and Fiji.
Highlight operators and tools in MiToBo
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CytoskeletonAnalyzer2D for the quantification of cytoskeleton structural patterns in microscopy images with texture measures;
to ease cell boundary extraction in data preparation we additionally provide the CellBoundaryExtractor2D and a handy LabelImageEditor
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PaCeQuant for quantifying the morphology and shape characteristics of cells
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Neuron Analyzer for the segmentation of neurons in microscope images
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Cell Migration Analyzer for analyzing single cell migration from time lapse image sequences
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Scratch Assay Analyzer for analyzing microscope images from collective cell migration experiments
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MiToBo for developers
MiToBo aims not only to support users in analyzing their images, but also targets at developers by offering a programmer-friendly software framework and API for developing new algorithms.
The MiToBo API completely separates the implementation of image processing algorithms from potential user interfaces based
on Alida which is a library for easing the development of data analysis
algorithms and tools. The main concept of Alida are operators as the core units for implementing data analysis algorithms.
Alida defines unified interfaces and execution procedures for operators which yield the fundament for its nice features like
- automatic documentation of complete analysis processes, e.g., leading from an input image to analysis results, in terms of processing graphs
- automatic generation of commandline and graphical user interfaces
- a graphical programming editor named Grappa automatically considering all implemented operators as potential processing nodes
MiToBo takes full advantage of Alida's features, hence, provides a framework for implementing image analysis algorithms allowing for automatic documentation and automatic user interface generation, and includes the graphical programming editor Grappa for user-friendly design of more complex processing pipelines.
