Software and Tools

Neuromantic

Neuromantic is a free application for the semi-manual or semi-automatic reconstruction of neurons for single images or image stacks. It is being developed primarily by Darren Myatt (d.r.myatt@reading.ac.uk) of the University of Reading. It is completely free to use for non-commercial purposes, such as academic research, although any commercial company wanting to licence it should get in touch. To date, Neuromantic has been downloaded hundreds of times from academic institutions worldwide, and generally averages about one download a day.

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Image J

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.

It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.

It does geometric transformations such as scaling, rotation and flips. Image can be zoomed up to 32:1 and down to 1:32. All analysis and processing functions are available at any magnification factor. The program supports any number of windows (images) simultaneously, limited only by available memory.

Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available.

ImageJ was designed with an open architecture that provides extensibility via Java plugins. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built in editor and Java compiler. User-written plugins make it possible to solve almost any image processing or analysis problem.

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Fiji

Fiji is an image processing package. It can be described as a "batteries-included" distribution of ImageJ (and ImageJ2), bundling Java, Java3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.  

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