Re: free hand cropping Z dimension

Posted by ctrueden on Sep 29, 2010; 9:07pm
URL: http://imagej.273.s1.nabble.com/free-hand-cropping-Z-dimension-tp3686762p3686763.html

Hi Matiar,

In Fiji's 3D Viewer you can do a free-hand "Fill selection" operation to
crop out portions of the data. For details, see:
  http://132.187.25.13/home/?category=Download&page=Viewer3D

The result will be that anything within the selection is blacked out in the
original image stack (which stays open in a separate window). You could then
run your analysis on that image stack and avoid picking up the undesired
spines.

HTH,
Curtis

On Wed, Sep 15, 2010 at 8:42 PM, Matiar Jafari <[hidden email]>wrote:

> Dear ImageJ List,
>
> I was wondering if anyone here knows of a way to crop free hand in the
> Z direction.  For example im analyzing dendritic spines and it would
> be a lot easier to automate the process if i was able to eliminate
> branches that go off in the Z as i do not want to analyze that branch.
>  A Z slice cropper would not suffice as it would crop part of the
> dendrite that I'm trying to analyze.  The program i deconvolve with
> allows me to do a freehand crop in the XY however not in the Z(only
> box), thus the solution would probably be to mess with the dimensions
> temporarily so that the ZY or ZX becomes the XY however i don't know
> how to do this.  Any ideas???
>
> Your help is greatly appreciated.
>
> Thank You
> -------
> Matiar Jafari
>