content of spots when cytoplasmic background is high

[Jacob Kerssemakers]

Dear All,

I'm trying to aply the very impressive SpotFinderZ tool to spots that are on top of a relatively high and increasing fluorescent level of the cytoplasm.
My impression is that this signal level (i.e., NOT the 'background level' outside the cells) is included in the fit, since my spot counts are many factors too high
I might be missing a proper setting.  Is there a way to correctly subtract such averaged levels before applying the spot fit?

Thanks a lot,

Jacob

[Anne Egholm Pedersen b]

Hello Jacob,

Have you tried changing the 'Fit area size, px' after clicking the Params button.  Let us know if this took care of your problem.


Regards,

Jacobs-Wagner Lab