Your Imagej Installation Cannot Be Updated Because It Is Read-only
A 4d dataset within ImageJ. [Original footage - Marker Sheffield; software development: Jeff Hardin]
I (Jeff) have developed plugins that run inside the public domain program, ImageJ, to acquire, process, and play dorsum 4d microscopy data as an outgrowth of our own imaging needs. The reward of this software suite is that information technology is free(!), and that it allows 4d datasets to exist viewed without special, proprietary software. Delight recognize that I am a professor, and program in my "spare" fourth dimension, and so back up for these plugins is express and bound to be sporadic!
Click on the links below to become to various sections of this page...
(one) MicroManager plugins for ImageJ(2) PerkinElmer plugins for ImageJ
(3) FRAP plugin for ImageJ
(four) Hyperstack Projector plugin (experimental)
(5) 4d video plugins
(6) ImageJ Macro toolsets
MicroManager scripts/plugins
Micro-Director to Hyperstack
: This plugin automates the creation of a Hyperstack from the Metadata.txt file of a Micro-Manager dataset. Caution: this plugin requires opening the dataset in RAM, due to a limitation in ImageJ's "Stack to Hyperstack…" command.
MM_Images_to_Hyperstack [source] [plugin]
Micro-Director 4d Beanshell script
: This Beanshell script runs in Micro-Manager, and replicates the bones functionality of our one-time 4d acquisition plugin running under ImageJ. Note: Due to all-encompassing enhancements in Micro-Managing director, we apply the Multi-Dimensional Conquering functionality built-in to Micro-Manager at present instead pif this older script. However, it prides a prissy example of integrating ImageJ calls into a M-Director script, and how to save out files with custom naming and location.
Download the source Beanshell script file [source]
Directions: Place in the ->scripts folder in your Micro-Manager installation. Open from the Micro-Manager Script panel, and click the "Run" button.
PerkinElmer Ultraview plugins
PE to Hyperstack plugin
: This plugin imports files from PerkinElmer Ultraview software into IMageJ as Hyperstacks. Due to limitations in ImageJ, only unmarried channel datasets can be imported as virtual hyper stacks (much faster, about no RAM load). Download this plugin as a JAR file: PE_to_Hyperstack.jar
Place the JAR file anywhere in the "Plugins" folder in your ImageJ installation. Restart ImageJ, and the plugins will announced under the "File/Import/PerkinElmer" carte du jour and in the "Plugins/PerkimElmer/" carte du jour in ImageJ. Source is independent in the JAR file, which tin be read using many archiving/unarchiving programs. We like Zipeg on Mac Os Ten.
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 programme Priism. This is a actually unintelligent plugin, but could be modified for other naming conventions.
Concatenate Movies [source] [plugin]
Description: This plugin reads movies from a specified binder and concatenates them in alphabetical order into one large moving picture. After using the Rename Perkin-Elmer AVIs plugin to rename them, this plugin is useful for concatenating .AVIs generated using Perkin-Elmer'due south UltraView software into a single 4d motion picture that tin can then be read using the QT4D Player plugin.
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FRAP plugins
FRAP profiler
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Updated October, 2018
: This plugin operates on a FRAP dataset (open in ImageJ every bit a TIFF stack). Normalizes for overall bleaching, and permits ane- and two-component exponential curve fitting (thank you to additions to ImageJ by Wayne Rasband; thanks Wayne!). Code written past Jeff Hardin, adjusted from Tony Collins' Macbiophotonics plugins.
Plugin is available hither: [source] [plugin]
Sample TIFF stack (ZIP annal; 53 Mb): sample information
Hyperstack Projector plugin
Hyperstack Projector
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Updated August, 2018 - Clarification: This is a crude attempt to imitate functionality in the onetime PerkinElmer Ultraview software. Adds a new menu option under the Hyperstacks submenu. This plugin operates on an ImageJ Hyperstack or Micro-Director multi-dimensional dataset window (which is based on the Hyperstack format), replacing the Hyperstack window with a new window in which a range of focal planes is projected on the fly. The original window is restored upon closing the projector window. Space bar toggles playback on/off, and arrow keys permit navigation in t and z (correct/left and up/down, respectively). Holding down the option central and using the right/left arrow keys switches channels. Space bar toggles playing of the flick. Requires ImageJ one.5 or college. Nether Micro-Manager 2.0 beta the hyperstack window cannot be hidden for reason I don't understand.
- Code written by Jeff Hardin. Source is in the JAR file. Suggestions for improvements are welcome!
Download this plugin equally a JAR file: Hyperstack_Projector.jar
meridian
QuickTime plugins
Note: This software is legacy software, since Apple has deprecated QuickTime for Coffee. Other even older legacy software is available on the Legacy software folio.
Notation : Many of these plugins were commented, streamlined, and nicely formatted years ago by my son, Jon Hardin (hardin@hardindd.com). He is President and CEO of his own company, Hardin Design and Development. Source code is freely available in the JAR file for all plugins.
Changelog:
- November 2014: Os X Yosemite (10.10) and greater no longer installs key files needed for QuickTime for Java. Fortunately, these tin be manually added to the correct locations to maintain the functionality of QTJ-dependent plugins under 32-bit ImageJ for OS X. Instructions and files tin be found here.
- May 2014: New versioning of the JVM and QuickTime necessitated an update for newest Mavericks (Mac Bone Ten 10.9) machines.
Download all plugins as a JAR file: 4d_Plugins.jar
Directions: Place the JAR file anywhere in the "Plugins" folder in your ImageJ installation. Restart ImageJ, and the plugins will appear nether various submenus in ImageJ, with names that correspond to the toolset macros provided on this page.
Documentation
Download "Installation Tips" [PDF]
Download the "Getting Started" guide with screen shots (2.7 Mb) [PDF]
QT4D Player [source] [plugin]
Clarification: This plugin displays 4d information saved as a QuickTime movie in a resizable ImageJ window. If nowadays, this plugin tin read information from a text file with the same root name as the 4d motion-picture show. The plugin allows export of images/stacks, and rudimentary processing of movies using standard QuickTIme filters (color, brightness/contrast, etc.). Works under Bone X and JVM 1.iv+ and QuickTime for Java 6.ane+. A Mac Bone nine version is available here: [source] [plugin]
QT4D Writer [source] [plugin]
Description: This plugin uses the same basic functionality as the QuickTime Stack Author plugin to compile a 4d moving-picture show from a folder containing 4d information as single images. Works under OS X and JVM 1.4+ and QuickTime for Coffee 6.ane+. A Mac Bone 9 version is available hither: [source] [plugin]
Browse4D [source] [plugin]
Description: This plugin allows browsing of 4d datasets created equally single images in a folder. Does not require reading the information into RAM or as a virtual stack, speeding initial admission times compared to the Image5D plugin or the Virtual Stack opener plugin.
A Mac OS 9 version is available here: [source] [plugin]
Update Dec. 2008: A bug in the info file reader routines was stock-still.
Update July 2009: Fixed focus trouble; changed shortcut keys to correspond to changes in ImageJ code base. Shift + left arrow = downwards; shift + right pointer = up;
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Image Macros/Toolsets
4d Tools toolset macro [source]
: This toolset macro installs a toolset for ImageJ that provides convenient button access to Jeff'southward QuickTime, 4d and rotation plugins. Identify in the ->macros->toolsets binder in your ImageJ home directory to enable this functionality. Requires ImageJ i.37t or higher.
Hyperstack 4d toolset for ImageJ
: This toolset macro installs a toolset for ImageJ that provides convenient button access to controlling Hyperstacks, and to the MM Images to Hyperstack plugin. Works under ImageJ 1.45s and later on (and likely somewhat before, just it hasn't been tested).Toolset assumes y'all've installed the MM_4d_Utilities.jar. To do: figure out how to get a clicked button in the macro toolset to repeatedly ship commands (like stepping upwardly/down, forrard/back).
Download the Hyperstack Tools toolset macro [source]
Directions: Place in the ->macros->toolsets folder in your ImageJ habitation directory to enable this functionality.
XY project macro [source]
Description: Performs 3d projection, stereo pair, and anaglyph project on a stack. Combines the functionality of the standard ImageJ 3d projection dialog with the stereo pair/anaglyph functions of Tony Collins' stereo pair plugin.
: Requires that the Stack Combiner plugin is installed.
Batch projection macro [source]
Description: Performs batch 3d projection on a folder of TIFF stacks, and outputs the results equally single images to some other directory. The resulting images can and then be compiled into a 4d QuickTime movies using the QT4D Writer plugin.
: Requires that the Stack Combiner plugin is installed.
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Support for farther evolution 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
Source: https://worms.zoology.wisc.edu/research/4d/4d.html
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