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=Viewer3DThe 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
>
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