Each time the acquisition button is pressed, a new image or image series is saved to the one file. The Leica LIF format is a database file format in which an individual file may contain multiple images (and image series) from a single experiment. An example of the development process reflects the collaborative nature of ImageJ development: when we took possession of our Leica TCS SP5 confocal, it came with yet another proprietary image format. This list is continually under development and is continually under development and is frequently updated the ImageJ community has been providing sample images. Recently the LOCI group from the University of Wisconsin has developed a bundled suite of plugins that will open over 65 image file formats from the biosciences (see a short list in Table 1 and their web site, for a complete list). This may include useful information, such as exposure settings and laser powers, but also essential settings such as pixel size, acquisition rate, and z-step-all required for proper interpretation of the data. Not only is the image data imported, the extra metadata is typically imported as well. The ability of ImageJ to open a wide variety of proprietary image formats has long been an important feature. ImageJ supports a wide number of standard image file formats, including the recent implementation 48-bit color composite imageJ support. Each of these approaches will match the installed ImageJ to the version described in the online MBF_ImageJ manual. Here, the appropriate version of ImageJ from the ImageJ homepage must be installed followed by a download of the plugins only MBF_ImageJ.zip file (which must be unzipped to a user's ImageJ folder). The second version is for non-Windows users. This includes a setup file that installs all of the required files. The first is a one-stop solution for Windows users. In the following discussion, I describe plugins included in the MBF ImageJ bundle (these are freely available on an individual basis elsewhere). The online manual provides links to original plugins and authors' pages. Users of the bundle are encouraged to cite the original authors of the plugins, who have been kind enough to make the results of their work freely available. The plugins are organized in submenus, and the bundle is described in an extensively illustrated online manual (which evolved from the original lab instructions). Here the package was resurrected as MBF ImageJ, containing all the plugins that I have found useful. When I recently joined the McMaster Biophotonics Facility (MBF at McMaster University, Hamilton, Canada, I was encouraged to maintain this ImageJ for Microscopy bundle. Initially collated from the ImageJ home page to help the Laboratory of Molecular Signaling in Babraham Institute (UK), I developed it further at the Wright Cell Imaging Facility (TWRI, Canada) here it was released as WCIF ImageJ. The ImageJ for Microscopy bundle and accompanying manual was developed to manage this wide-ranging array of plugins. Once saved to the ImageJ plugins folder, these functions are loaded on start-up and can be accessed via menu commands like any other core function. These additional files are either written in Java (the plugins) or in ImageJ's macro programming language (macros). While Rasband is the author of the core program, an extensive group of additional developers has written and made available a growing arsenal of short add-on programs to provide additional functionality to the core program. ![]() However, a few steps into ImageJ, and this minor inconvenience is forgotten. One of the downsides of the Java heritage is an interface that may feel a little unfamiliar. The new 64-bit operating systems and their JRE have happily broken the long-held 1.7 Gb memory limit for Java applications. With JRE available for most operating systems, ImageJ is platform-independent, running on Macintosh, Windows, Linux, and even a PDA operating system. Java runtime environments (JRE) are freely available, either from Sun or bundled with platform-specific installations of ImageJ ( /ij). To run ImageJ, a given system needs only the operating system-specific Java runtime environment. By shifting to Java, Rasband liberated the software from an individual operating system. Wayne Rasband is the core author of ImageJ after developing the Macintosh-based National Institutes of Health (NIH) Image for 10 years, he made the brave decision of starting afresh with ImageJ using the Java programming language. In addition to its impressive functionality, this cutting-edge image-processing tool has an indispensable support community of enthusiasts on the ImageJ mailing list. These past 10 years have seen the Java-based open-source software mature into an invaluable laboratory tool. ImageJ will celebrate its tenth anniversary in September of this year.
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