Help - on-the-fly HyperStack Projector

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Help - on-the-fly HyperStack Projector

Jeff Hardin-2
Dear ImageJ colleagues,,
I hope you’re all well. I’m emailing in the hope that someone might enjoy improving a bit of code for doing HyperStack projections on the fly. I tried this a number of years ago, but it was terrible. Now it sort of works and does what I want, and has a reasonable interface.

A JAR of the current version is here: Hyperstack_Projector.jar<>
It installs a “HyperStack Projector” menu item in the “HyperStacks” submenu. If you go get the “Mitosis" multichannel Hyperstack file, it will run on that to give you a sense for what I’m after.

This plugin tries to recreate in a crude fashion the functionality of the old Perkin-Elmer UltraView software, which would display moving Z projections on the fly from 4d datasets.  This assumes an ImageJ Hyperstack. The plugin relies on hiding the original Hyperstack window after grabbing its ImagePlus, removing the original window from the Window Manager menu,  and then at the end restoring the hidden window. Inelegant, but it works.

The plugin requires ImageJ >=1.5. It also works in Micro-Manager 1.4.22 if one upgrades its jar to 1.5. The main hyperstack window  can't be hidden (as far as I can tell!) in Micro-Manager 2.0, but otherwise it works.

Currently this code implements projections as single images that overwrite the image in an ImageWindow from single time point Z stacks, rather than overloading the drawing routines of ImageJ's Hyperstack class, which is probably what should be done.  As a result, composite images don't work currently. I replicated similar looking controls so it feels mostly like a HyperStack.

The ZProjector routines  seem to return colored images, so If “Grayscale" is selected in the main window, these are set to gray using a Channel tool routine before being displayed. This is crude!

The .java file of the current draft version is in the JAR file. I’d like to add composite functionality.

I hope someone can point me to a programmer who really knows their Hyperstacks. I guess Marcel Boeglin did some helpful code additions in 2013 to the ZProjector class. Does anyone possibly have his contact information?

Alternatively, if I’m missing another plugin that has this functionality, please point me in the right direction.

Thanks in advance for your help.
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Integrative Biology
Faculty Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
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