ImageJ

ImageJ

Overview
ImageJ is a public domain, Java
Java (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

-based image processing
Image processing
In electrical engineering and computer science, image processing is any form of signal processing for which the input is an image, such as a photograph or video frame; the output of image processing may be either an image or, a set of characteristics or parameters related to the image...

 program developed at the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...

. ImageJ was designed with an open architecture
Open architecture
Open architecture is a type of computer architecture or software architecture that allows adding, upgrading and swapping components. For example, the IBM PC and Apple IIe have an open architecture, whereas the Apple IIc and Amiga 500 computers have a closed architecture...

 that provides extensibility
Extensibility
In software engineering, extensibility is a system design principle where the implementation takes into consideration future growth. It is a systemic measure of the ability to extend a system and the level of effort required to implement the extension...

 via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological
Radiology
Radiology is a medical specialty that employs the use of imaging to both diagnose and treat disease visualized within the human body. Radiologists use an array of imaging technologies to diagnose or treat diseases...

 image processing, multiple imaging system data comparisons to automated hematology
Hematology
Hematology, also spelled haematology , is the branch of biology physiology, internal medicine, pathology, clinical laboratory work, and pediatrics that is concerned with the study of blood, the blood-forming organs, and blood diseases...

 systems. ImageJ's plugin architecture and built in development environment has made it a popular platform for teaching image processing.

ImageJ can be run as an online applet
Applet
In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page...

, a downloadable application, or on any computer with a Java 5 or later virtual machine
Virtual machine
A virtual machine is a "completely isolated guest operating system installation within a normal host operating system". Modern virtual machines are implemented with either software emulation or hardware virtualization or both together.-VM Definitions:A virtual machine is a software...

.
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Encyclopedia
ImageJ is a public domain, Java
Java (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

-based image processing
Image processing
In electrical engineering and computer science, image processing is any form of signal processing for which the input is an image, such as a photograph or video frame; the output of image processing may be either an image or, a set of characteristics or parameters related to the image...

 program developed at the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...

. ImageJ was designed with an open architecture
Open architecture
Open architecture is a type of computer architecture or software architecture that allows adding, upgrading and swapping components. For example, the IBM PC and Apple IIe have an open architecture, whereas the Apple IIc and Amiga 500 computers have a closed architecture...

 that provides extensibility
Extensibility
In software engineering, extensibility is a system design principle where the implementation takes into consideration future growth. It is a systemic measure of the ability to extend a system and the level of effort required to implement the extension...

 via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological
Radiology
Radiology is a medical specialty that employs the use of imaging to both diagnose and treat disease visualized within the human body. Radiologists use an array of imaging technologies to diagnose or treat diseases...

 image processing, multiple imaging system data comparisons to automated hematology
Hematology
Hematology, also spelled haematology , is the branch of biology physiology, internal medicine, pathology, clinical laboratory work, and pediatrics that is concerned with the study of blood, the blood-forming organs, and blood diseases...

 systems. ImageJ's plugin architecture and built in development environment has made it a popular platform for teaching image processing.

ImageJ can be run as an online applet
Applet
In computing, an applet is any small application that performs one specific task that runs within the scope of a larger program, often as a plug-in. An applet typically also refers to Java applets, i.e., programs written in the Java programming language that are included in a web page...

, a downloadable application, or on any computer with a Java 5 or later virtual machine
Virtual machine
A virtual machine is a "completely isolated guest operating system installation within a normal host operating system". Modern virtual machines are implemented with either software emulation or hardware virtualization or both together.-VM Definitions:A virtual machine is a software...

. Downloadable distributions are available for Microsoft Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...

, Mac OS
Mac OS
Mac OS is a series of graphical user interface-based operating systems developed by Apple Inc. for their Macintosh line of computer systems. The Macintosh user experience is credited with popularizing the graphical user interface...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, and the Sharp Zaurus PDA
Sharp Zaurus
The Sharp Zaurus is the name of a series of Personal Digital Assistant made by Sharp Corporation. The Zaurus was the most popular PDA during the 1990s in Japan and was based on a proprietary operating system. The first Sharp PDA to use the Linux operating system was the SL-5000D, running the...

. The source code for ImageJ is freely available.

The project developer, Wayne Rasband, is at the Research Services Branch of the National Institute of Mental Health
National Institute of Mental Health
The National Institute of Mental Health is one of 27 institutes and centers that make up the National Institutes of Health...

.

Features


ImageJ can display, edit, analyze, process, save, and print 8-bit
8-bit color
8-bit color graphics is a method of storing image information in a computer's memory or in an image file, such that each pixel is represented by one 8-bit byte. The maximum number of colors that can be displayed at any one time is 256....

, 16-bit and 32-bit images. It can read many image formats including TIFF, PNG, GIF
GIF
The Graphics Interchange Format is a bitmap image format that was introduced by CompuServe in 1987 and has since come into widespread usage on the World Wide Web due to its wide support and portability....

, JPEG
JPEG
In computing, JPEG . The degree of compression can be adjusted, allowing a selectable tradeoff between storage size and image quality. JPEG typically achieves 10:1 compression with little perceptible loss in image quality....

, BMP, DICOM, FITS
FITS
Flexible Image Transport System is a digital file format used to store, transmit, and manipulate scientific and other images. FITS is the most commonly used digital file format in astronomy...

, as well as raw formats. ImageJ supports image stacks, a series of images that share a single window, and it is multithreaded, so time-consuming operations can be performed in parallel on multi-CPU hardware. ImageJ can calculate area and pixel value statistics of user-defined selections and intensity thresholded objects. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as logical and arithmetical operations between images, contrast manipulation, convolution
Convolution
In mathematics and, in particular, functional analysis, convolution is a mathematical operation on two functions f and g, producing a third function that is typically viewed as a modified version of one of the original functions. Convolution is similar to cross-correlation...

, Fourier analysis, sharpening, smoothing
Smoothing
In statistics and image processing, to smooth a data set is to create an approximating function that attempts to capture important patterns in the data, while leaving out noise or other fine-scale structures/rapid phenomena. Many different algorithms are used in smoothing...

, edge detection and median filtering
Median filter
In signal processing, it is often desirable to be able to perform some kind of noise reduction on an image or signal. The median filter is a nonlinear digital filtering technique, often used to remove noise. Such noise reduction is a typical pre-processing step to improve the results of later...

. It does geometric transformations such as scaling
Scaling
Scaling may refer to:* Scaling , a linear transformation that enlarges or diminishes objects* Reduced scales of semiconductor device fabrication processes...

, rotation and flips. The program supports any number of images simultaneously, limited only by available memory.

History


Prior to the release of ImageJ in 1997, a similar freeware image analysis program known as NIH Image had been developed for Macintosh computers running pre-Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

 operating systems. Further development of this code continues in the form of Image SXM
Image SXM
Image SXM is an image analysis software specialized in scanning microscope images. It is based on the public domain NIH Image and extended to handle scanning microscope images, especially of the SxM formats , hence its name.- Features :Image SXM supports image stacks, a series of images that...

, a variant tailored for physical research of scanning microscope images. A Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...

 version – ported
Porting
In computer science, porting is the process of adapting software so that an executable program can be created for a computing environment that is different from the one for which it was originally designed...

 by Scion Corporation, so called Scion Image for Windows – was also developed. Both versions are still available.

See also

  • Microscope image processing
    Microscope image processing
    Microscope image processing is a broad term that covers the use of digital image processing techniques to process, analyze and present images obtained from a microscope. Such processing is now commonplace in a number of diverse fields such as medicine, biological research, cancer research, drug...

  • Fiji (Fiji Is Just ImageJ)
    FIJI (software)
    Fiji is an Open Source image processing package based on ImageJ.Fiji's main purpose is to provide a distribution of ImageJ with many bundled plugins. As with Ubuntu, Fiji has an integrated updating system...

    , an image processing package based on ImageJ
  • Rapidminer Image Processing Extension - tool for image processing and image mining
  • Bitplane
    Bitplane
    Bitplane is a provider of software for 3D and 4D image analysis for the life sciences. Founded in December 1992, Bitplane operates out of two offices in Zürich, Switzerland and one in South Windor, CT, USA.- Company history :...

     - producers of image processing software with ImageJ compatibility
  • CoLocalizer Pro
    CoLocalizer Pro
    CoLocalizer Pro is a scientific software application, developed by , that allows researchers to analyze colocalization in the images obtained using fluorescence microscopy. Due to high popularity of Macintosh computers in medicine and biology, the software is designed specifically for Mac OS X...

     - software application for quantification of colocalization in fluorescence microscopy images

External links


Distributions

  • ImageJ for Microscopy - from the McMaster
    McMaster University
    McMaster University is a public research university whose main campus is located in Hamilton, Ontario, Canada. The main campus is located on of land in the residential neighbourhood of Westdale, adjacent to Hamilton's Royal Botanical Gardens...

     Biophotonics Facility
  • Fiji (Fiji is Just ImageJ): An ImageJ bundled distribution; many scripting languages supported (see Scripting). Fiji focuses on image registration, stitching, segmentation and 3D visualization.

Plug-ins


NIH Image