Bioimage informatics

ThunderSTORM is an open-source, interactive, and modular plug-in for ImageJ designed for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. Our philosophy in developing ThunderSTORM has been to offer an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data.

This is an ImageJ plugin to analyze bacterial cells. It provides a user-friendly interface and a powerful suite of detection, analysis and data presentation tools. It works with individual phase or fluorescence images as well as stacks, hyperstacks, and folders of any of these types. Even large image sets are analyzed rapidly generating raw tabular data that can either be saved or copied as is, or have additional statistical analysis performed and graphically represented directly from within MicrobeJ, making it an all-in-one image analysis solution.

It is a tool to visualize and annotate volume image data of electron microscopy. Users can annotate objects (e.g. neurons) and skeleton structures. It provides the ability to overlaying the image data with user annotations, representing the spatial structure and the connectivity of labeled objects, and displaying a three dimensional model of it. It can be extended by plugins written in python. A similar, web-based implementation is being developed at webknossos.info. Example datasets are also available.

MorphoLibJ is a library of plugin for ImageJ with functionalities for image processing such as filtering, reconstructing, segmenting, etc... Tools are based on Mathematical morphology with more rigorous mathematical approach than in the standard tools of ImageJ in particular for surface (or perimeter) measurements which are usually based on voxel counting.  

http://imagej.net/MorphoLibJ#Measurements

Among the features:

Morphological operations :  Dilation, Erosion, Opening,  Closing , Top hat (white and black), Morphological gradient (aka Beucher Gradient), Morphological Laplacian, Morphological reconstruction, Maxima/Minima , Extended Maxima/Minima -Watershed (classic or controlled) -Image overlay -Image labelling -Geodesic diameter -Region Adjacency Graph -Granulometry curves, morphological image analysis.

Calculate the Fourier ring correlation (FRC). The FRC can be used as a resolution criterion for super resolution microscopy. The Plugin can display a plot of the FRC curve, along with the LOESS smoothed version of the curve. Finally it displays the threshold method used and the intersection of the FRC with the threshold, providing the FIRE number. It can be used on two open images or on pairs of images in batch mode. 2654 2655