THE HARDIN LABClick on the links below to go to various sections of this page...
Micro-Manager 4d Beanshell scriptDescription: This Beanshell script runs in Micro-Manager, and replicates the basic functionality of our old 4d acquisition plugin running under ImageJ. Note: Due to extensive enhancements in Micro-Manager, we use the Multi-Dimensional Acquisition functionality built-in to Micro-Manager now instead of this older script. However, it provides a nice example of integrating ImageJ calls into a M-Manager script, and how to save out files with custom naming and location.
Download the source Beanshell script file [source]
Perkin-Elmer Plugins for ImageJ
PE to Hyperstack plugin
Description: This plugin imports files from PerkinElmer Ultraview software into ImageJ as Hyperstacks. Due to limitations in ImageJ, only single channel datasets can be imported as virtual hyper stacks (much faster, almost no RAM load).
Download this plugin as a JAR file: PE_to_Hyperstack.jar
Directions: Place the JAR file anywhere in the "Plugins" folder in your ImageJ installation. Restart ImageJ, and the plugins will appear under the "File/Import/PerkinElmer" menu and in the "Plugins/PerkimElmer/" menu in ImageJ. Source is contained in the JAR file, which can be read using many archiving/unarchiving programs. We like Zipeg on Mac OS X.
Rename PerkinElmer Ultraview AVIs [source] [plugin]
Description: This plugin adds leading zeros to the names of Perkin-Elmer AVIs produced from Perkin-Elmer's UltraView temporal module software for the Perkin-Elmer LCI spinning disc confocal microscope. This allows them to be concatenated alphabetically into 4D movies using the Concatenator plugin.
Rename PerkinElmer Ultraview TIFFs [source] [plugin]
Description: This plugin renames TIFF stacks for use with the Linux-based program Priism. This is a really unintelligent plugin, but could be modified for other naming conventions.
Concatenate Movies [source] [plugin]
Description: This plugin reads movies from a specified folder and concatenates them in alphabetical order into one large movie. After using the Rename Perkin-Elmer AVIs plugin to rename them, this plugin is useful for concatenating .AVIs generated using Perkin-Elmer's UltraView software into a single 4d movie that can then be read using the QT4D Player plugin.
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QuickTime Plugins for ImageJThe only way to run QuickTime for Java (QTJ) is on older machines with older operating systems. Most IT departments do not want older machines on the internet for security reasons, so these solution often require crippling internet access.
These plugins do work in emulators, as far back as Mac OS 9 (using Sheepshaver or UTM; tested as late as August 2025!).
Many Quicktime plugins for ImageJ used to be found on the ImageJ plugins page at the ImageJ website. Thanks to Wayne Rasband (NIH) for writing the base code for ImageJ, and for hosting and annotating plugins. Wayne is a tireless servant of the biomedical imaging community.
Note: Many of these plugins were commented, streamlined, and nicely formatted years ago by my son, Jon Hardin when he was a kid. Jon is a computer scientist and President and CEO of his own company, Hardin Design and Development. Source code is freely available in the JAR file for all plugins.
Documentation (circa 2007)
Download "Installation Tips" [PDF]
Download the "Getting Started" guide with screen shots (2.7 Mb) [PDF]
Important notes
(1) Quicktime for Java has long been deprecated by Apple. It does not function on 64-bit installations of ImageJ. This means that you must be running ImageJ in 32-bit mode. Quicktime for Java does not work at all on Windows systems running in 64-bit mode.
(2) OS X Yosemite and later no longer does an install of QuickTime for Java. Please see this page for help.
(3) July 2011: Recent Java updates required changes to the version checking code in these plugins. Try the most recent versions of the plugins on this site if you are having trouble. The 4d_Plugins.jar file has been updated.
(3) QuickTime plugins require that QuickTime for Java (QTJ) is installed on your computer. Requires both QuickTime and QuickTime for Java. Both were preinstalled on Macs as late as the 2010s.. Windows users had to install QuickTime 7 and copy QTJava.zip to the Java extensions folder (ImageJ\jre\lib\ext). Additional instructions are here.
(4) Older issues
(a) Changes to the underlying architecture of QuickTime for Java broke many pieces of code under Mac OS X when using JMV 1.4+ and QTJ 6.1+. I have rewritten a ton of code to allow my plugins to work on newer Macs. An invaluable resource is Chris Adamson's book, QuickTime for Java: A Developer's Notebook (O'Reilly). In addition to the book, Chris is a really cool guy and incredibly helpful to the QuickTime for Java developer community.
(b) Oct. 2007: The latest update to QuickTime (7.2) can result in non-functional QuickTime for Java when a Mac was updated first using the QuickTime 7.2 updater and then the OS X 10.4.10 combined updater. The latter overwrites some newer QTJ files that are installed as part of the QuickTime 7.2 update. Downloading the QuickTime 7.2 updater as a standalone application at http://www.apple.com/support/downloads/quicktime72formac.html and reinstalling the QuickTime 7.2 update seems to fix this problem on the occasional machine I have encountered that displays this behavior.
(c) Oct. 2007: The latest update to QuickTime (7.2) can result in non-functional QuickTime for Java when a Windows machine has more than one version of the Java Runtime Environment (JRE) or the Java Development Kit (JDK). Apple's automatic update software for QuickTime only updates the QTJava.zip file associated with the newest version of the Java Virtual Machine installed. This means that for QTJava calls to function after updating to QuickTime for Windows 7.2 or higher, you must manually replace the QTJava.zip file associated with each older JVM.
(d) May 2014: New versioning of the JVM and QuickTime necessitated an update for newest Mavericks (Mac OS X 10.9) machines.
QuickTime plugins available on the ImageJ web site
QuickTime Movie Player [removed]
Description: This plugin played a QuickTime movie in a window with a standard movie controller. Original code by Wayne Rasband; updated by Jeff Hardin for newer implementations of QTJ. Works under OS X and JVM 1.4+ and QuickTime for Java 6.1+.
Note: Wayne Rasband has implemented similar changes to the built-in QuickTime movie player in ImageJ. Use "File->Import...->QuickTime Movie..." under most recent version of ImageJ
QuickTime Movie Opener [removed]
Description: This plugin opens a QuickTime movie as an ImageJ stack. Original code by Wayne Rasband; updated by Jeff Hardin for newer implementations of QTJ. Works under OS X and JVM 1.4+ and QuickTime for Java 6.1+.
Note: Wayne Rasband has implemented similar changes to the built-in QuickTime movie player in ImageJ. Use "File->Import...->Using QuickTime..." under most recent version of ImageJ
QuickTime Video Capture [removed]
Description: Previews and captures video frames from a QuickTime compatible camera. Written by Wayne Rasband, with minor help for newer implementations of QTJ by Jeff Hardin. Works under OS X and JVM 1.4+ and QuickTime for Java 6.1+.
Note: This is now built-in to ImageJ. Use "File->Import...->Video." under most recent version of ImageJ for Mac OS X.
QuickTime Stack Writer
Description: This plugin is an alternative to the QuickTime Movie Writer plugin that comes with ImageJ. It uses the QuickTime native Save As... dialog box, which means it cannot be as easily scripted using the Macro recorder in ImageJ. It is dramatically faster that the Movie Writer plugin. Works under OS X and JVM 1.4+ and QuickTime for Java 6.1+. By Jon and Jeff Hardin.
You can also pick it up here: [source] [plugin]
JMF Movie Player
Description: This plugin displays uncompressed AVIs using Sun's Java Media Framework. This plugins works under Windows, Mac OS 9, Mac OS X, and Linux. jmf.jar must be installed in the appropriate location. Note that in theory this plugin could serve as the basis of Linux-friendly 4d player for uncompressed AVIs. We have tried to get this working, but we have a long way to go...
Other QuickTime and 4d Plugins
Source code can be edited with any text editor or ImageJ itself. Plugins are packaged as .ZIP files. Unzip using your compression software of choice (e.g., WinZip or StuffIt Expander), and place in the Plugins directory (or subfolder) within the ImageJ directory.
QuickTime Movie Player (revised) [source] [plugin]
Description: This plugin plays a QuickTime movie in a resizable window with a standard movie controller. Original code by Wayne Rasband; updated by Jeff Hardin for newer implementations of QTJ. Works under OS X and JVM 1.4+ and QuickTime for Java 6.1+.
Concatenate Movies [source] [plugin]
Description: This plugin reads movies from a specified folder and concatenates them in alphabetical order into one large movie. After using the Rename Perkin-Elmer AVIs plugin to rename them, this plugin is useful for concatenating .AVIs generated using Perkin-Elmer's UltraView software into a single 4d movie that can then be read using the QT4D Player plugin.
Legacy acquisition plugins for ImageJ
Acquire4D
Description: This plugin has been used in the Hardin lab for acquiring 4d Nomarski data using a Ludl MAC2000 Z controller with Uniblitz shutter, or a Prior Optiscan Z controller with a DTR-controlled Uniblitz shutter. Images are acquired from a video source using a Scion AG5 frame grabber. The Scion libraries and ImageJ files should be installed as described here. Z controllers and shutters are controlled through the serial port (or using a USB-to-serial adapter, such as the Keyspan adapter) using the easy-to-use SerialIO serial port libraries. Operating system-specific versions of this library can be purchased from SerialIO. Works under OS X and JVM 1.4+ and QuickTime for Java 6.1+. A Mac OS 9 version is available.
Two slightly different versions of this plugin are available:
(1) Ludl MAC2000 Z-motor/Uniblitz D122 controlled via the Ludl [source] [plugin]
A Mac OS 9 version [source] [plugin]
(2) Prior Optiscan Z-motor/Uniblitz D122 controlled via the data terminal ready (DTR) line of a custom serial cable. Mac OS 9 version, but should be adaptable for OS X/Windows [source] [plugin]
Legacy software for Mac OS 9
NIH Image 1.62-QTS
Application and macros as a Stuffit .sit file for MAC2000 : [application bundle]
[source code (in Pascal!) available on request]
Description: Modified version of NIH Image for Mac OS 9 or below. This version has added functionality for improved serial port control, data terminal ready line (DTR) control, and compilation of QuickTime movies from single-image 4d datasets.
Support for development of some of these plugins was provided through the National Institutes of Health and National Science Foundation
