WatershedCounting3D (Also StackViewer: see below)

Segment/count fluorescent objects identified by local maxima in 3D confocal image data even with inhomogeneous background and clustering. This program uses the maximum gradient within each watershed region to separate background objects from objects of interest.

As described in Traffic for segmenting/counting ER exit-sites and Golgi (Gniadek T, Warren G):

http://www.blackwell-synergy.com/doi/abs/10.1111/j.1600-0854.2006.00538.x

This ImageJ plug-in is freely available for academic users. Please cite the above paper when referencing this plug-in.

Download: WatershedCounting3D.jar (right click, Save Target As. Updated 03/19/07)

Note: Windows may change the file extension to WatershedCounting_3D.ZIP

If this happens, simply rename the file WatershedCounting_3D.JAR

Instructions: WatershedCounting3D_Instructions.txt (right click, Save Target As)

ImageJ: http://rsb.info.nih.gov/ij/ or http://en.wikipedia.org/wiki/ImageJ

Update Notes …

03/19/07 Problem Fixed: On certain OS versions, graphic output is a black single image unless zoomed out.

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StackViewer

Free Add-In for cine viewing 3D data sets in PowerPoint with instructions: http://www.stackviewer.com

Gniadek TJ, Desjardins B. Interactive display of stacks of images in scientific presentations with PowerPoint. AJR Am J Roentgenol. 2004 Sep;183(3):859-61.

Download the plug-in for your operating system (right click, Save Target As)

Windows XP

Windows 2000

Mac OS X

Question, Comments: thomas.gniadek@yale.edu