Rename PerkinElmer Ultraview AVIs ĭescription: 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. Source is contained in the JAR file, which can be read using many archiving/unarchiving programs. Restart ImageJ, and the plugins will appear under the "File/Import/PerkinElmer" menu and in the "Plugins/PerkimElmer/" menu in ImageJ. Due to limitations in ImageJ, only single channel datasets can be imported as virtual hyper stacks (much faster, almost no RAM load).ĭownload this plugin as a JAR file: PE_to_Hyperstack.jarĭirections: Place the JAR file anywhere in the "Plugins" folder in your ImageJ installation. Open from the Micro-Manager Script panel, and click the "Run" button.ĭescription: This plugin imports files from PerkinElmer Ultraview software into IMageJ as Hyperstacks. However, it prides a nice example of integrating ImageJ calls into a M-Manager script, and how to save out files with custom naming and location.ĭownload the source Beanshell script file ĭirections: Place in the ->scripts folder in your Micro-Manager installation. Note: Due to extensive enhancements in Micro-Manager, we use the Multi-Dimensional Acquisition functionality built-in to Micro-Manager now instead pif this older script. MM_Images_to_Hyperstack ĭescription: This Beanshell script runs in Micro-Manager, and replicates the basic functionality of our old 4d acquisition plugin running under ImageJ.
Caution: this plugin requires opening the dataset in RAM, due to a limitation in ImageJ's "Stack to Hyperstack…" command. (4) Hyperstack Projector plugin (experimental)ĭescription: This plugin automates the creation of a Hyperstack from the Metadata.txt file of a Micro-Manager dataset. Please recognize that I am a professor, and program in my "spare" time, so support for these plugins is limited and bound to be sporadic!Ĭlick on the links below to go to various sections of this page. The advantage of this software suite is that it is free(!), and that it allows 4d datasets to be viewed without special, proprietary software.
I (Jeff) have developed plugins that run within the public domain program, ImageJ, to acquire, process, and play back 4d microscopy data as an outgrowth of our own imaging needs.
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