Posted by
mirrownight on
Mar 02, 2016; 10:10am
URL: http://imagej.273.s1.nabble.com/deconvolution-problem-tp5001407p5015765.html
Hi Brian
I had the same question with Amy, too. Thank you for the suggestion about
flipping the PSF.
But I have other problems using the "Batch" module. I tried to load the
image stacks like showed in the photo:
<
http://imagej.1557.x6.nabble.com/file/n5015763/Forum.png>
But failed to run deconvolution even all the images were 2D tiff.
And the dimension of the PSF was smaller than the image stacks.
Is there any file format limitation for the "Batch" module?
Thanks,
Mirrownight
bnorthan wrote
> Hi Amy
>
> Yes as far as I know all the algorithms in Deconvolution Lab need the
> PSF to be shifted.
>
> In terms of papers if you want something general I would recomend the
> following.
>
> Biggs, S. C., “A practical guide to deconvolution of fluorescence
> microscope imagery,” Microscopy Today 18(1), 10-14 (2010).
>
> In terms of specific details for DeconvolutionLab... they implement a
> few algorithms. Richardson Lucy is the basic one. Richardson Lucy
> with TV Regularization and Thresholded Landweber are more advanced.
> They should produce better results but have more complicated input
> parameters. I tried them a couple of times before but didn't get the
> result I expected. Though I personally haven't had a chance to work
> with those algorithms much and figure out the right settings. Maybe
> someone else has more experience with them?? You should keep asking
> around. The references for those algorithms are below....
>
> Dey, N., Bland-Feraud L., Zimmer, C., Roux, P., Kam, Z., Olivo-Marin,
> J.-C., and Zerubia, J., “Richardson-Lucy algorithm with total
> variation regularization for 3D confocal microscope deconvolution,”
> Microscopy Research and Technique, 69, 260-266 (2006).
>
> Vonesch, C. and Unser, M., “A fast thresholded Landweber algorithm for
> wavelet-regularized multidimensional deconvolution,” IEEE transactions
> on image processing, 17(4), 539-549 (2008).
>
> On Fri, Jan 18, 2013 at 3:43 PM, Amy Cao <
> amycao723@
> > wrote:
>> Hi Brian,
>>
>> Is that mean all the algorithms in Deconvolution Lab require the center
>> of
>> the PSF to be 0,0,0?
>>
>> Sorry about this simple question, because I am not doing the algorithms
>> things, and I always confused about that. Is it possible for you maybe to
>> recommend some papers about this deconvolution so that I can get some
>> ideas
>> about it?
>>
>> Thank you so much,
>>
>> Jianwei Cao
>>
>> On Thu, Jan 17, 2013 at 6:50 AM, Brian Northan <
> bnorthan@
> > wrote:
>>
>>> Hi Amy
>>>
>>> Yes. The equations in the deconvolution consider the center of the
>>> PSF to be 0,0,0. While on the other hand in an image the center is
>>> ussually at width/2, height/2, depth/2. So flip PSF moves the
>>> coordinate system to where the algorithm needs it to be.
>>>
>>> Brian
>>>
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>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>
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