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superresolved.com • View topic - Plugin/macro to open directly a 3B reconstruction

Plugin/macro to open directly a 3B reconstruction

Bayesian analysis of blinking and bleaching

Plugin/macro to open directly a 3B reconstruction

Postby morales » Tue Sep 17, 2013 7:03 pm

Hi again!
It is actually quite neat to have the control panel, and is very useful to set the reconstruction blur FWHM to see the effect on each reconstruction. However once I've decided for a certain blur, I was wondering if there was a way to open directly an image file without going trough the control panel. I reckon it would be very useful for a macro that I'm writing which automatically assembles 3B reconstructions of small contiguous ROIs into a larger reconstructed area.

Thanks in advance.
morales
 
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Re: Plugin/macro to open directly a 3B reconstruction

Postby edrosten » Mon Sep 23, 2013 12:39 pm

edrosten
 
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Re: Plugin/macro to open directly a 3B reconstruction

Postby edrosten » Tue Sep 24, 2013 3:45 pm

edrosten
 
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Re: Plugin/macro to open directly a 3B reconstruction

Postby morales » Thu Sep 26, 2013 6:39 pm

morales
 
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Re: Plugin/macro to open directly a 3B reconstruction

Postby edrosten » Fri Sep 27, 2013 1:30 pm

edrosten
 
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Re: Plugin/macro to open directly a 3B reconstruction

Postby morales » Mon Oct 14, 2013 9:52 am

morales
 
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Re: Plugin/macro to open directly a 3B reconstruction

Postby edrosten » Fri Nov 01, 2013 5:21 pm

edrosten
 
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Re: Plugin/macro to open directly a 3B reconstruction

Postby morales » Thu Nov 07, 2013 2:02 pm

Thanks! I'll give it a try.
morales
 
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Re: Plugin/macro to open directly a 3B reconstruction

Postby chal.nikkal » Mon Jan 12, 2015 12:59 pm

In the manual it says: "If possible, placing the boundary near a bright region should be avoided. If this is not possible, then the reconstruction close to the boundary should be ignored." When we concatenate the file as you suggest, should we be careful in interpreting any fluorescence coming from pixels close to the boundary of the individual ROIs??
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Re: Plugin/macro to open directly a 3B reconstruction

Postby edrosten » Fri Jan 23, 2015 10:57 am

Yes, in general you need to be very careful about using data near the boundary.

If the region is too large and you cannot avoid the boundary then the solution is to split the region up into a grid of overlapping masks. That way data from near the edge of the mask can be rejected without leaving gaps in the final reconstruction. There are some instructions and programs described here which will help:

viewtopic.php?f=10&t=30218

Note that you'll need one of the beta releases of 3B in order to use this feature.

-Ed
edrosten
 
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