selecting detections in Colocalization studio plugin

[Greta Schachermayer]

Hello, 

I am quite new to ICY and sometimes get stuck on little things, so apologies for the stupid question...

My problem is: I want to do an object based colocalization analysis using colocalization studio but can't select any detections for the analysis. 

Here is what I did: 

I first extracted channel 1 of my original 3 channel z-stack, ran the spot detector on it, using the settings: Force use  of 2D wavelets for 3D, scale 3 (7 px) sensitivity 50. I chose the option no filtering and for display I deselected "project all detections of a same stack" (maybe that makes a difference?). 

Then I did the exact same thing for channel 2 of the original z-stack. 

All the files were automatically saved in the saves folder, and i left the windows with the spot-detected images open in ICY. 

Now when I go on to the colocalization studio plugin it won't let me select anything for Detections 1 and Detections 2. However, when I go to the correlation option (rather than object based analysis) the plugin does give me the option to select both sequences for channel 1 and channel 2. 

I did run the colocalization studio plugin once before and it worked. I am not sure what I did differently. 

Thank you very much in advance for your help!

Kindly, 

Greta 

[Stephane]

Hi Greta,

Actually you need to enable a specific option in the spot detector so others plugins can access the detections result :
In the "output" tab, just enable "export to swimming pool" before doing the detection.

I guess the colocalization studio documentation missed that point ;) You have it through Spot Detector documentation but i admit it was not easy to figure it out ;)
http://icy.bioimageanalysis.org/plugin/Spot_Detector

Best,

- Stephane

[thibault...@yahoo.fr]

Dear Greta,

I would just like to mention that Colocalization Studio is designed for 2D images, 3D is coming..

Best,

Thibault Lagache

Le jeudi 4 décembre 2014 19:37:18 UTC+1, Greta Schachermayer a écrit :

[Greta Schachermayer]

Dear Stephane and Thibault, 

Thank you very much for your help. It's working now! Looking forward to the §D addition for colocalization studio now. 

All the best, 

Greta