colocalization functions

[Giuliana Fossati]

Dear all,
I'm a neuroscientist working in the University of Milan, Italy.
I have two problems with my data analysys and maybe you can give me a very huge help.

1)I need to study colocalization between pre- and postsynaptic markers. For this purpose I use the "AND" operation or the "colocalization" plugin, but in this way I can obtain only puncta in which there's an overlapping between the two markers.
However, it is not always necessary that two markers overlap to constitute a synapse, either for the focal plane or for the structure of the synapse itself.
Then this is the point: is it possible to obtain an implementation in the program to consider not only overlapping puncta, but also puncta very close one each other, for example puncta separated by 0.005um?

2)The second problem is actually related to the previous one. Very often I need to do triple colocalization, and the plugin "colocalization" is able to colocalize only two fluorescence channels, is it possible to improve the plugin for colocalizing three channels once?

Thank you very much

Best regards

Giuliana

[Albert Cardona-2]

On Jan 8, 2012, at 2:41 PM, Giuliana Fossati <[hidden email]> wrote:

> Dear all,
> I'm a neuroscientist working in the University of Milan, Italy.
> I have two problems with my data analysys and maybe you can give me a very huge help.
>
> 1)I need to study colocalization between pre- and postsynaptic markers. For this purpose I use the "AND" operation or the "colocalization" plugin, but in this way I can obtain only puncta in which there's an overlapping between the two markers.
> However, it is not always necessary that two markers overlap to constitute a synapse, either for the focal plane or for the structure of the synapse itself.
> Then this is the point: is it possible to obtain an implementation in the program to consider not only overlapping puncta, but also puncta very close one each other, for example puncta separated by 0.005um?


You could scale down the image so that then the separate parts of the same synape overlap. Otherwise it's a tough segmentation problem.


> 2)The second problem is actually related to the previous one. Very often I need to do triple colocalization, and the plugin "colocalization" is able to colocalize only two fluorescence channels, is it possible to improve the plugin for colocalizing three channels once?


You could AND two channels and then AND the result with the third. Same with the collocalization plugin: if channel 1 colocs with ch 2, and 2 with 3 , then 1 with 3 too.

Otherwise contract a developer to extend the program to you specifications.

Albert



>
> Thank you very much
>
> Best regards
>
> Giuliana

[Thomas Boudier]

Hello Giuliana,

This is the king of things that collegues are doing, they are using my
3d spots segmentation for segmenting synaptic markers and then the
3Droimanager to compute distances or colocalization between objects.
Contact me for more detailed help.

Thomas

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start



Le 08/01/2012 20:41, Giuliana Fossati a écrit :

> Dear all,
> I'm a neuroscientist working in the University of Milan, Italy.
> I have two problems with my data analysys and maybe you can give me a very huge help.
>
> 1)I need to study colocalization between pre- and postsynaptic markers. For this purpose I use the "AND" operation or the "colocalization" plugin, but in this way I can obtain only puncta in which there's an overlapping between the two markers.
> However, it is not always necessary that two markers overlap to constitute a synapse, either for the focal plane or for the structure of the synapse itself.
> Then this is the point: is it possible to obtain an implementation in the program to consider not only overlapping puncta, but also puncta very close one each other, for example puncta separated by 0.005um?
>
> 2)The second problem is actually related to the previous one. Very often I need to do triple colocalization, and the plugin "colocalization" is able to colocalize only two fluorescence channels, is it possible to improve the plugin for colocalizing three channels once?
>
> Thank you very much
>
> Best regards
>
> Giuliana
>
>

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