http://imagej.273.s1.nabble.com/Deconvolution-Lab-Batch-Module-tp5015776p5018982.html
happening. A while back someone had a similar problem, and it turned out
it was caused by a scale bar that had been drawn on the image. You can
And take a look at the statistics of the image. The total sum should be
> yes...it has become more sharper...and i have given normalize psf too!!
>
> but the intensity of deconvolved image is totally different...deconvolved
> images are more dark...and when i am trying to adjust the brightness and
> intensity of true and deconvolved images, they never match...
>
> the true image appears to have more brightness...the intensity is between 0
> and 255... for the other it is just 0.
>
>
> so how can i compare it...
> i wanted to check their snr too..
> is there any other parameter that i can check to acess the quality
> improvement??
>
> On Wed, Jun 28, 2017 at 5:05 PM, bnorthan [via ImageJ] <
>
[hidden email]> wrote:
>
> > Hi Ash
> >
> > The dynamic range of a deconvolved image will be larger. So the output
> > probably will not scale to 8 bit.
> >
> > Also make sure you click the option 'normalize PSF'. This will make the
> > PSF is normalized to unit energy, and that will mean you can directly
> > compare input and output values.
> >
> > The deconvolved image should have sharper and higher peaks. This is
> > because blurry "wide" features, should now be narrower and more intense.
> >
> > Brian
> >
> > On Wed, Jun 28, 2017 at 7:06 AM, Ash <[hidden email]
> > <
http:///user/SendEmail.jtp?type=node&node=5018980&i=0>> wrote:
> >
> > > i got results..thanks..one more doubt!!
> > > my input image was 8 bits..after deconvolution size is becoming 32
> > > bits...how do i convert output images intensity to that of input
> image??
> > >
> > > i want to compare the images...but since intensities are varying i m
> not
> > > able to compare!!
> > >
> > > On Sun, Jun 25, 2017 at 11:46 PM, Ash Fairy <[hidden email]
> > <
http:///user/SendEmail.jtp?type=node&node=5018980&i=1>> wrote:
> > >
> > > > Thank you, I will do that. ..
> > > > Well can I send it to your mail id?
> > > >
> > > > On Jun 25, 2017 6:16 PM, "bnorthan [via ImageJ]"
> > <ml+s1557n5018964h66@n6.
> > > > nabble.com> wrote:
> > > >
> > > >> Hi Ash
> > > >>
> > > >> If I understand you correctly, you need to directly deconvolve the
> > > image.
> > > >> The microscope has already approximately convolved the true object
> > with
> > > >> the
> > > >> PSF.
> > > >>
> > > >> If you are able to share the image and bead image, I am happy to try
> > and
> > > >> deconvolve them, and let you know the best approach and settings.
> > > >>
> > > >> Brian
> > > >>
> > > >> On Sun, Jun 25, 2017 at 12:09 AM, Ash <[hidden email]
> > > >> <
http:///user/SendEmail.jtp?type=node&node=5018964&i=0>> wrote:
> > > >>
> > > >> > so before going to deconvolutionLab plugin, first do we have to
> > > >> convolve
> > > >> > the image and its PSF?? And then compare results of image
> convolved
> > > >> with
> > > >> > PSF , with the end result of that blurred image with PSF???
> > > >> >
> > > >> > Or are we directly starting to deconvolve image that we have taken
> > and
> > > >> its
> > > >> > PSF???
> > > >> >
> > > >> > On Sat, May 27, 2017 at 5:19 PM, bnorthan [via ImageJ] <
> > > >> > [hidden email] <
http:///user/SendEmail.jtp?
> > > type=node&node=5018964&i=1>>
> > > >> wrote:
> > > >> >
> > > >> > > Hi Ash
> > > >> > >
> > > >> > > If you are using deconvolution lab, it should automatically
> > resize
> > > >> the
> > > >> > PSF
> > > >> > > in x and y. If I recall correctly deconvolution lab does not
> > resize
> > > >> in
> > > >> > z.
> > > >> > > So you should make the PSF x by y by 37 (z same z in image).
> > Make x
> > > >> and
> > > >> > y
> > > >> > > the right size to contain one bead. Make sure the bead is
> > centered.
> > > >> > >
> > > >> > > I also would subtract the background level (at least subtract
> the
> > > min
> > > >> > > value
> > > >> > > of the cropped bead image).
> > > >> > >
> > > >> > > If you are able to share any images I can give it a try.
> > > >> > >
> > > >> > > On Wed, May 24, 2017 at 4:54 AM, Ash <[hidden email]
> > > >> > > <
http:///user/SendEmail.jtp?type=node&node=5018792&i=0>> wrote:
> > > >> > >
> > > >> > > > hii
> > > >> > > > thank you for replying me..yes..i do have multiple bead...the
> > psf
> > > >> has
> > > >> > 99
> > > >> > > > frames and image has 37 frames....if i am cropping a single
> > bead
> > > >> out
> > > >> > > then
> > > >> > > > how should i adjust the size to make it compatible with the
> raw
> > > >> > > > image???because raw images size is 2048*2048 and bead size is
> > > >> > > 512......if i
> > > >> > > > crop out a single bead, then the bead file will become more
> > > >> smaller!!!
> > > >> > > >
> > > >> > > > On Tue, May 23, 2017 at 8:00 PM, bnorthan [via ImageJ] <
> > > >> > > > [hidden email] <
http:///user/SendEmail.jtp?
> > > >> > type=node&node=5018792&i=1>>
> > > >> > > wrote:
> > > >> > > >
> > > >> > > > > Hi Ash
> > > >> > > > >
> > > >> > > > > If you can share your image and psf I can try and help you.
> > > From
> > > >> > your
> > > >> > > > > description I suspect your image contains multiple beads.
> To
> > > use
> > > >> it
> > > >> > > as a
> > > >> > > > > PSF you would have to crop out one bead.
> > > >> > > > >
> > > >> > > > > Brian
> > > >> > > > >
> > > >> > > > > On Mon, May 15, 2017 at 5:45 PM, Ash <[hidden email]
> > > >> > > > > <
http:///user/SendEmail.jtp?type=node&node=5018778&i=0>>
> > wrote:
> > > >> > > > >
> > > >> > > > > > my input image size is 2048*2048*37 and psf size is
> > > >> > > 512*512*99....how
> > > >> > > > > > should
> > > >> > > > > > i resize it?do i have to do fft or ifft to get
> > deconvolution
> > > >> > > > result..the
> > > >> > > > > > psf
> > > >> > > > > > file that i have contain several beads....should i take
> > > average
> > > >> of
> > > >> > > all
> > > >> > > > > the
> > > >> > > > > > beads in that file to deconvolution.... or just uploading
> > the
> > > >> psf
> > > >> > > file
> > > >> > > > > with
> > > >> > > > > > sveral beads is fine?
> > > >> > > > > > i am doing with deconvolution lab software...how should i
> > > >> proceed?
> > > >> > > > > >
> > > >> > > > > >
> > > >> > > > > >
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