Posted by
bnorthan on
Sep 20, 2013; 6:45pm
URL: http://imagej.273.s1.nabble.com/DeconvolutionLab-Batch-Processing-tp5004865p5004883.html
One PSF file should work for them all assuming similar acquisition
conditions.
The PSF is actually a little bit different for each location within one
image. That is because the PSF is determined by the path the light takes
through the sample, and the refractive index of the sample (and for a real
sample the RI will be different throughout).
Assuming one PSF for the image is a "approximation" that is used for most
deconvolution algorithms (unless you get into algorithms that use special
schemes to subdivide the image). Likewise assuming one PSF for the entire
set is fine assuming all images were taken under similar settings.
How are you getting the PSF?? A bead image??
On Fri, Sep 20, 2013 at 1:04 PM, mehulmvora <
[hidden email]> wrote:
> Hi Brian
>
> Thank you for your reply. I'm a complete newbie to deconvolution and
> confocal microscopy.
>
> I don't have individual PSF files for each of the images - isn't that
> what's required? Each image is different from the rest (but they were taken
> at the same time with the same scope and settings). Will one PSF file work
> for them all? I thought that each image will have it's own psf?
>
> Thank you!
>
>
> On Fri, Sep 20, 2013 at 12:52 PM, bnorthan [via ImageJ] <
>
[hidden email]> wrote:
>
> > Hi
> >
> > Do you have the PSF image open?? I've done this before and I needed to
> > open
> > the PSF image, go to the PSF option, then select "Flip PSF Quadrants" (if
> > the PSF is centered). After that select the input and output folders.
> >
> > It should then process all the files using the same PSF.
> >
> > Brian
> >
> >
> > On Thu, Sep 19, 2013 at 5:52 PM, mehulmvora <[hidden email]<
>
http://user/SendEmail.jtp?type=node&node=5004880&i=0>>
> > wrote:
> >
> > > Hello
> > >
> > > I wish to use DeConvolutionLab to perform batch processing on a number
> > of
> > > .tiff stacks.
> > >
> > > I can choose the Input and Output folders without a problem. When I hit
> > RUN
> > > it will show me the Initial input files and the new output file names.
> > >
> > > However, it asks me for PSF file.
> > >
> > > When I do them individually, I use the same file as both input and
> > output.
> > > But am not sure how to do this for batch?
> > >
> > > Any help appreciated. I have 100s of files to process ! :)
> > >
> > >
> > >
> > > --
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