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Abràmoff Et Al., 2004 - Image Processing With Image J
Abràmoff Et Al., 2004 - Image Processing With Image J
Image Processing
with ImageJ
by Dr. Michael D. Abràmoff, University of Iowa Hospitals and Clinics; Dr. Paulo J. Magalhães,
University of Padua; and Dr. Sunanda J. Ram, Louisiana State University Health Sciences Center
T
he advances of the medical and bi- search areas, from nanotechnology to as- The program is the brainchild of Wayne
ological sciences over recent years, tronomy. Rasband of the Research Services Branch,
and the growing importance of de- It is common practice for manufactur- National Institute of Mental Health, in
termining the relationships between struc- ers of image acquisition devices to include Bethesda, Md. It is called ImageJ because
ture and function, have made imaging an dedicated image processing software, but it is written in the Java language. Its first
increasingly important discipline. The these programs are usually not very flex- release, version 0.50, was Sept. 23, 1997,
ubiquitousness of digital technology — ible and/or do not allow more complex and it is now in version 1.31, released in
from banal digital cameras to highly spe- image manipulations. Image processing February.
cific micro-CT scanners — has made im- programs also are available by themselves. According to the institute, it has been
ages an essential part of a number of re- ImageJ holds a unique position because downloaded from its Web site tens of
Reprinted from the July 2004 issue of Biophotonics International © Laurin Publishing Co. Inc.
IMAGING SOFTWARE
Figure 3. This simple ImageJ macro for (i = 0; i < 5; i++) //5 frames
acquires an image every 10 seconds
and stores it in sequence. next = getTime ()+ 10 * 1000; //10s between frames
//Run plug-in that grabs from a Quicktime framegrabber
run (“QT Capture”, “grab”);
Cell Imaging Facility at Toronto Western while (getTime) () < next) wait (1); //until 10s are over.
Research Institute. This free, very thor-
ough manual has many examples and il-
lustrations. It emphasizes microscopy and Macros are meant to make it easier to exist in core capabilities of ImageJ. Once
accompanies a collection of microscopy- automate oft-repeated tasks, which would implemented, they cannot be distin-
related plug-ins. Although many open- be tedious to implement manually. guished from the program itself. A small
source programs lack an extensive user ImageJ has an easy-to-use macro-language cottage industry has sprouted from users/
manual, even novices can find most of that means that knowledge of Java isn’t developers who are designing plug-ins
the information for their imaging needs required for writing simple scripts. For for their own use and sharing them with
in this manual. example, a macro can be written that ac- all users. Plug-ins have brought ImageJ
quires an image every 10 seconds and from an image processing program to a
Extensions: Macros and plug-ins stores it in a sequence (Figure 3). framework that scientists can use to de-
The program is virtually limitless be- Plug-ins are external programs, mostly velop their own imaging solutions.
cause of the availability of user-written written in the Java language, that offer Plug-ins range from very small and
macros and plug-ins. image processing capabilities that do not straightforward, such as the Grid plug-in
— which simply draws a grid on an image
— to complex, practically stand-alone
TABLE
image programs, such as the dendrite-
Image formats supported by ImageJ as of June 2004
tracing tool NeuronJ1 or the surface and
Format Read and write volume-rendering plug-in VolumeJ.2 In
fact, the standard imaging capabilities
Analyze (Mayo Clinic’s format) (plug-in) that ImageJ comes with are implemented
AVI uncompressed movies as plug-ins as well. Developing new plug-
Bio-Rad Z-series (plug-in) ins requires knowing Java language and is
BMP thus not for everyone.
DICOM (uncompressed) read However, after using ImageJ for a while,
DICOM (uncompressed) write (plug-in)
users often need a specific solution for
DM3 (Gatan Corp. transmission electron microscopy format) (plug-in)
their problem that goes beyond its core ca-
FDF, VFF (Varian MRI imaging system/EVS 900 micro-CT system (plug-in)
formats) pabilities. The Medientechnik und design
FITS (NASA format) read group in Austria has written a tutorial
GIF (including animated) specifically as an introduction to writing
ICO, CUR (MS Windows) (plug-in) plug-ins for ImageJ.
IPLab (Scanalytics Corp. microscopy format) (plug-in) Most plug-ins that are judged by their
Jpeg developers to be of general use can be
Jpeg EXIF digital camera header (plug-in) published on the ImageJ Web site, which
Leica SP multichannel (plug-in) now holds more than 150 plug-ins, writ-
LSM (Zeiss LSM 510 confocal microscopes) (plug-in)
ten by 98 developers. Some developers
PCX (Zsoft Corp.) (plug-in)
may instead make their plug-ins and
PDS (Planetary Data System) (plug-in)
PGM (P2 and P5) read macros available through personal Web
PICT (Apple Mac) (plug-in) sites; some of these are listed on the
PNG ImageJ site.
PSD (Adobe Photoshop) (plug-in)
QuickTime movies Imaging library
Raw (any uncompressed file format not directly supported, A third way of extending ImageJ, which
8-,16-, 24-bit RGB, 32-bit, small- and big-endian) is used by only a small number of more
SIF (Andor Technology spectroscopy format) (plug-in) technically advanced developers, is to use
SPE format (Roper Scientific cameras) (plug-in)
its imaging capabilities and plug-ins from
Sunraster (plug-in)
their own programs, so that, in technical
Targa (plug-in)
Text images (tab or comma separated) terms, they are using it as a library of imag-
Tiff uncompressed and zip compressed, both as ing methods. This is called ImageJ’s ap-
1-, 8-, 12-, 16-bit unsigned, 32-bit (real) plication programmer’s interface (API),
or RGB color, single and multiple images (stacks) which has been extensively documented
XBM, XPM (X-Windows formats) (plug-in) so that it is clear how to use and carry
XLS (Microsoft Excel) (plug-in) out these methods. This way, several
online image database servers have been
IMAGING SOFTWARE
Figure 7. The EyeCheck Web site provides online diabetic retinopathy screening
from retinal color photographs. The left area of the image shows the Web page
with patient information. When this page is accessed, an ImageJ applet
automatically displays the retinal photographs (in this case, of a normal subject),
at right. This allows for user interaction so that, for example, the intensity image
can be displayed, as in the bottom part, or specific abnormalities can be marked.
Courtesy of EyeCheck.
IMAGING SOFTWARE
Web Resources
• rsb.info.nih.gov/ij — ImageJ and most of its plug-ins and macros are available for download.
• www.uhnres.utoronto.ca/wcif/download.html — ImageJ manual by Tony Collins.
• mtd.fh-hagenberg.at/depot/imaging/imagej — The Medientechnik und design group tutorial on writing plug-ins.
• imagescience.bigr.nl/meijering/software/neuronj — NeuronJ is available for download.
• bij.isi.uu.nl — Web site for VolumeJ and many other biomedical imaging plug-ins.