The Hardin Lab

Legacy plugins/code
Many Quicktime plugins for ImageJof these plugins can 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.

Important notes
(1) Quicktime for Java is being 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 no longer does an install of QiuickTime 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 are preinstalled on Macs. Windows users must install QuickTime 7 and copy QTJava.zip to the Java extensions folder (ImageJ\jre\lib\ext). Additional instructions can be found here on the ImageJ web site.

(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 further development of some of these plugins was provided through a software development supplement to a grant from the National Institutes of Health and an equipment supplement to a grant from the National Science Foundation

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