Counting items over stacks

[mkii]

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[Markus Krieger]

Hi there,
I´m looking for a tool to count dendritic spines in z-stacks with.
Cell counter plugin was not well suited because labels stick to pic in which they were added.
This requires jumping back and forth through stack to check whether spines were already counted in previous layers.
Makes my head swim.
Would need labels to remain visible as I go through stack.
Anybody with a good tool, or an easy way to modify CC plugin?
MK

[Gabriel Lapointe-2]

Hello Markus,
When I used to do something similar I always started by making a maximum
projection of the stack then activated the cell counter plugin on the
projection. The trick is to finally synchronize the images. Then, any
click in the stack will be marked on the projection.

Cheers

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Gabriel Lapointe, M.Sc.
6651 de Lanaudière, app
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Montréal (Québec), H2G
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http://gabriellapointe.ca










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On Tue, 2011-02-01 at 13:39 +0100, Markus Krieger wrote:

> Hi there,
> I´m looking for a tool to count dendritic spines in z-stacks with.
> Cell counter plugin was not well suited because labels stick to pic in which they were added.
> This requires jumping back and forth through stack to check whether spines were already counted in previous layers.
> Makes my head swim.
> Would need labels to remain visible as I go through stack.
> Anybody with a good tool, or an easy way to modify CC plugin?
> MK

[mkii]

Maximum projection didn´t help much, I tried that before.
Too many spines were lost upon projection.

Problem has been solved with neuromantic software which keeps labels while scrolling through stacks conveniently by moving mouse up/down. It´s actually intended for reconstructive tracking of whole neurons, but it works here as well.

Thanks for the input

-mk