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Re: calculating DF/F and movement correction

Posted by Jacob Keller on Aug 10, 2012; 4:16pm
URL: http://imagej.273.s1.nabble.com/calculating-DF-F-and-movement-correction-tp4999726p4999730.html

Yes! this is it! To make this plugin align all imags to a single image, one
just sets the "template update coefficient" to 1, and no adjustments are
made to the template. Excellent! Thanks Kees,

Jacob

On Fri, Aug 10, 2012 at 10:56 AM, Straatman, Kees R. (Dr.) <
[hidden email]> wrote:

> Did you have a look at the image stabilizer plugin (
> http://www.kangli.org/code/Image_Stabilizer.html)?
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Centre for Core Biotechnology Services
> University of Leicester
> http://www.le.ac.uk/biochem/microscopy/home.html
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Jacob Keller
> Sent: 10 August 2012 16:35
> To: [hidden email]
> Subject: Re: calculating DF/F and movement correction
>
> If you get an answer for the movement correction question, I would love to
> hear it--I have been trying to do this for some time. You can try StackReg,
> but for me, since it works by a "moving window" approach to image
> alignment, errors seem to accumulate and the sample moves slowly over
> hundreds of images. If there were some way to align each image to a "master
> image" that would be much better for our purposes.
>
> Jacob
>
>
> On Fri, Aug 10, 2012 at 9:28 AM, Nicolás Pírez <[hidden email]
> >wrote:
>
> > Dear List,
> >
> >
> >
> > I am new at using ImageJ. I am using it to measure the changes in
> > fluorescence in a stack (time lapse). I have been using the ROIManager
> and
> > Multimeassure to obtain the fluorescence levels.
> >
> > I have two questions: is there a function to calculate the DF/F
> > automatically? - eg: [(Fn/F0)/F0]X100%.
> >
> >
> >
> > Additionally, I would like to be able to measure this value even in where
> > is some drift in the ROI across different slices in the stack (all images
> > are of the same field, but there is some movement X-Y). Is there a
> movement
> > correct function, so that the ROI can "follow" the movement?
> >
> >
> >
> > Thanks a lot,
> >
> >
> > Nicolás Pírez.
> >
> > --
> > Nicolás Pírez, Ph.D.
> > [hidden email]
> >
> > Fundación Instituto Leloir, Lab. 109.
> > Av. Patricias Argentinas 435
> > Ciudad de Buenos Aires (C1405BWE)
> > Argentina
> > Phone +54 (11) 5238-7500 ext: 2109
> > Fax +54 (11) 5238-7501
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: [hidden email]
> *******************************************
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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>



--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
*******************************************

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