analyzing spine dynamics in ImageJ

[Reena Prity Murmu]

I am interested in analyzing spine dynamics/turnover. At present we do  
not have any software to  do that. I have heard that it is possible to  
analyze spine dynamics in ImageJ  by measuring spine length over time.  
Since, I have never done this kind of analyses before, It would be  
great if someone could tell me which ImageJ plugins are required to  
perform such analyses, i.e. measure spine length or study spine  
dynamics over time
many thanks
Reena
Lund, Sweden

[suendermann]

Dear Reena,

in principal you don't need any plugin to analyse spine length. I don't
know which kind of data you have, so I assume you have a 2D timeseries
of spine images. For a manual analysis you just have to define a point
on the base of the spine neck as a starting point and the furthest point
on the spine head. Then connect both via line-tool and press crtl-m for
measurement.
I'm not aware of any automatical analysis tool.

Greetings
   Fred

On 26.10.2010 17:05, Reena Prity Murmu wrote:

> I am interested in analyzing spine dynamics/turnover. At present we do
> not have any software to  do that. I have heard that it is possible to
> analyze spine dynamics in ImageJ  by measuring spine length over time.
> Since, I have never done this kind of analyses before, It would be
> great if someone could tell me which ImageJ plugins are required to
> perform such analyses, i.e. measure spine length or study spine
> dynamics over time
> many thanks
> Reena
> Lund, Sweden

[Reena Prity Murmu]

Dear Fred,
  The data that I want to analyze are Z-stacks of dendritic segments  
taken at different time points. Will try what u suggested in ImageJ.  
Thank u very much for ur suggestion.

Best wishes
Reena

On Oct 27, 2010, at 8:23 AM, suendermann wrote:

> Dear Reena,
>
> in principal you don't need any plugin to analyse spine length. I  
> don't
> know which kind of data you have, so I assume you have a 2D timeseries
> of spine images. For a manual analysis you just have to define a point
> on the base of the spine neck as a starting point and the furthest  
> point
> on the spine head. Then connect both via line-tool and press crtl-m  
> for
> measurement.
> I'm not aware of any automatical analysis tool.
>
> Greetings
>   Fred
>
> On 26.10.2010 17:05, Reena Prity Murmu wrote:
>> I am interested in analyzing spine dynamics/turnover. At present we  
>> do
>> not have any software to  do that. I have heard that it is possible  
>> to
>> analyze spine dynamics in ImageJ  by measuring spine length over  
>> time.
>> Since, I have never done this kind of analyses

[Michael Schell]

Hi Reena,

For motilty studies, the Matus group used a routine where they  
subtracted successive time-lapse frames and keep pixel values that  
change  between frames.  You can do this with Stacks-TFunctions-
DeltaFDown plugin from the MBF plugin collection.  We've used a  
variation of this where you project the deltaF stack using Stacks-
Zproject-standard deviation to create a 2D image of motilty.  Before  
doing this be sure the timelapse stack is well aligned  (stacks-
shuffling-align slices).

Another excellent plugin is NeuronJ, which facilitates protrusion  
length measurements.  There a many more clever things people have done  
with ImageJ and spines scattered in the literature.

Michael

On Oct 27, 2010, at 4:26 AM, Reena Prity Murmu wrote:

> Dear Fred,
> The data that I want to analyze are Z-stacks of dendritic segments  
> taken at different time points. Will try what u suggested in ImageJ.  
> Thank u very much for ur suggestion.
>
> Best wishes
> Reena