Introduction of ImageJ: The software we use to process the obtained fluorescent videos

ImageJ is a public domain Java image processing and analysis 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 1.5 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’ (and hyperstacks), 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.
ImageJ is being developed on Mac OSX using its built in editor and Java compiler, plus the BBEdit
editor and the Ant build tool. The source code is freely available. The author, Wayne Rasband
(wsr@nih.gov), is a Special Volunteer at the National Institute of Mental Health, Bethesda,
Maryland, USA.