Help for Wavelet spot detector in Protocols

[François L. (MNHN)]

Hi there,

I wanted to use Wavelet spot detector with Protocols. I get the online protocol called "Colocalizer" which is working fine.

But I want to use ROI to detect special regions in cells (ie nucleus with Hoechst) and then detect spots only in these ROIs.

I get ROIs with the "Thresholder" box but I don't know how to use ROIs with the spot detector block (I didn't find a way to use ROIs with "Compute WAT considering ROI"). Is there a way to connect this two boxes ?

Thanks a lot !

François L.

[Fabrice de Chaumont]

Dear Francois,

The Wavelet block detects spots over all the image. It can use the rois as an input to compute the noise estimation over those roi, but the output still a binary image over the complete image. Then the connected component is used to 'create' the spots, and finally the exporters sorts the output of the connected components per ROIs.

I hope this is clearer with those info.

Best,

Fabrice

[Jeremy Pike]

Hi

I am trying to do the same thing as Francois. I have used connected components to create the spots but cant figure out how to export the spots per ROI? If I select "BACKGROUND" within connected components then I get not reference to ROIs in the exported excel document. If I select ROI then get no information about the spots.

I have attached the protocol.

Thank you for any help.

Jeremy