Collection

Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer has more than one workflow available for neuron tracing. 

"The Neural Circuit Tracer is open source software built using Java (Sun Microsystems) and Matlab (MathWorks, Inc., Natick MA). It is based on the core of ImageJ (http://rsbweb.nih.gov/ij) and the graphic user interface has been developed by using Java Swings. The software combines anumber of functionalities of ImageJ with several newly developed functions for automated and manual tracing of neurites. The Neural Circuit Tracer is designed in a way
that will allow the users to add any plug-ins developed for ImageJ. More importantly, functions written in MatLab and converted into Java with Matlab JA toolbox can also be added to the Neural Circuit Tracer." 

Microscopy Image Browser (MIB) is a high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.

MIB is a freely available, user-friendly software for effective image processing of multidimensional datasets that improves and facilitates the full utilization of acquired data and enables quantitative analysis of morphological features. Its open-source environment enables fine tuning and possibility of adding new plug-ins to customize the program for specific needs of any research project.

MorphoGraphX is a free Linux application for the visualization and analysis of 3D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 3D live-imaged confocal data sets.

The main research interests adressed by MorphoGraphX are:

• Shape extraction
• Growth analysis
• Signal quantification
• Protein localization

hIPNAT (hIPNAT: Image Processing for NeuroAnatomy and Tree-like structures) is a set of tools for the analysis of images of neurons and other tree-like morphologies. It is written for ImageJ, the de facto standard in scientific image processing. It is available through the ImageJ Neuroanatomy update site.

CIDRE is a retrospective illumination correction method for optical microscopy. It is designed to correct collections of images by building a model of the illumination distortion directly from the image data. Larger image collections provide more robust corrections. Details of the method are described in

K. Smith, Y. Li, F. Ficcinini, G. Csucs, A. Bevilacqua, and P. Horvath
CIDRE: An Illumination Correction Method for Optical Microscopy, Nature Methods 12(5), 2015, doi:10.1038/NMETH.3323