Standardized test image sets for deconvolution

[leavesley]

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Hi All,

Does anyone know if there are standardized zstack image sets (with
corresponding PSFs) available for testing deconvolution algorithms?  Thanks!

Best regards,

Silas

--
Silas J. Leavesley, Ph.D.
Professor
Department of Chemical and Biomolecular Engineering
Department of Pharmacology
Center for Lung Biology
University of South Alabama
150 Jaguar Drive, SH4129
Mobile, AL 36688
ph: (251)-460-6160
fax: [phone]
web: http://www.southalabama.edu/centers/bioimaging

[Brian Northan]

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Hi Silas

You could look at the website for DeconvolutionLab2, they have several real
and synthetic datasets... though they only have theoretical PSFs and no sub
resolution bead images, which is unfortunate because it would be nice to be
able to compare Deconvolution results between theoretical PSF, and a PSF
derived from beads.

http://bigwww.epfl.ch/deconvolution/index.html#data

I also recommend the DeconvolutionLab2 paper.  It has a nice summary and
some comparisons of the most widely used algorithms.

http://bigwww.epfl.ch/deconvolution/deconvolutionlab2/sage1701p.pdf

Brian

On Tue, Oct 15, 2019 at 12:12 PM Silas Leavesley <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi All,
>
> Does anyone know if there are standardized zstack image sets (with
> corresponding PSFs) available for testing deconvolution algorithms?
> Thanks!
>
> Best regards,
>
> Silas
>
> --
> Silas J. Leavesley, Ph.D.
> Professor
> Department of Chemical and Biomolecular Engineering
> Department of Pharmacology
> Center for Lung Biology
> University of South Alabama
> 150 Jaguar Drive, SH4129
> Mobile, AL 36688
> ph: (251)-460-6160
> fax: [phone]
> web: http://www.southalabama.edu/centers/bioimaging
>

[leavesley]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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*****

Hi Brian,

Thanks and this is indeed a very helpful set of tools and example datasets!

Best regards,

Silas

On 10/15/2019 2:33 PM, Brian Northan wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Silas
>
> You could look at the website for DeconvolutionLab2, they have several real
> and synthetic datasets... though they only have theoretical PSFs and no sub
> resolution bead images, which is unfortunate because it would be nice to be
> able to compare Deconvolution results between theoretical PSF, and a PSF
> derived from beads.
>
> http://bigwww.epfl.ch/deconvolution/index.html#data
>
> I also recommend the DeconvolutionLab2 paper.  It has a nice summary and
> some comparisons of the most widely used algorithms.
>
> http://bigwww.epfl.ch/deconvolution/deconvolutionlab2/sage1701p.pdf
>
> Brian
>
> On Tue, Oct 15, 2019 at 12:12 PM Silas Leavesley <[hidden email]>
> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Hi All,
>>
>> Does anyone know if there are standardized zstack image sets (with
>> corresponding PSFs) available for testing deconvolution algorithms?
>> Thanks!
>>
>> Best regards,
>>
>> Silas
>>
>> --
>> Silas J. Leavesley, Ph.D.
>> Professor
>> Department of Chemical and Biomolecular Engineering
>> Department of Pharmacology
>> Center for Lung Biology
>> University of South Alabama
>> 150 Jaguar Drive, SH4129
>> Mobile, AL 36688
>> ph: (251)-460-6160
>> fax: [phone]
>> web: http://www.southalabama.edu/centers/bioimaging
>>

--
Silas J. Leavesley, Ph.D.
Professor
Department of Chemical and Biomolecular Engineering
Department of Pharmacology
Center for Lung Biology
University of South Alabama
150 Jaguar Drive, SH4129
Mobile, AL 36688
ph: (251)-460-6160
fax: [phone]
web: http://www.southalabama.edu/centers/bioimaging

[Nathan-64]

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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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*****

Hi all!

It would be great to have a test set of images that included:

1. a phantom (i.e., target) image

2. that same phantom with the effects of Gaussian+Poisson noise and a
theoretical PSF imposed (i.e., simulating imaging by a microscope+camera.)

3. A sufficiently sampled 3D microscopic image with reporters in multiple
wavelengths

4. Theoretical PSF's corresponding with 3 (e.g., from Gibson and Lani, etc.)

5. Empirical PSFs corresponding with 3

I'd also love to see what some of the recent CNN and other machine learning
methodologies could do with such data.

NOTE: I am employed by a commercial entity, but we don't develop
deconvolution solutions. I'm just interested in this topic as it was an
area of research I was involved in ~100 years ago :)

Best,
Nate




On Tue, Oct 15, 2019 at 5:50 PM Silas Leavesley <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Brian,
>
> Thanks and this is indeed a very helpful set of tools and example datasets!
>
> Best regards,
>
> Silas
>
> On 10/15/2019 2:33 PM, Brian Northan wrote:
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > Post images on http://www.imgur.com and include the link in your
> posting.
> > *****
> >
> > Hi Silas
> >
> > You could look at the website for DeconvolutionLab2, they have several
> real
> > and synthetic datasets... though they only have theoretical PSFs and no
> sub
> > resolution bead images, which is unfortunate because it would be nice to
> be
> > able to compare Deconvolution results between theoretical PSF, and a PSF
> > derived from beads.
> >
> > http://bigwww.epfl.ch/deconvolution/index.html#data
> >
> > I also recommend the DeconvolutionLab2 paper.  It has a nice summary and
> > some comparisons of the most widely used algorithms.
> >
> > http://bigwww.epfl.ch/deconvolution/deconvolutionlab2/sage1701p.pdf
> >
> > Brian
> >
> > On Tue, Oct 15, 2019 at 12:12 PM Silas Leavesley <
> [hidden email]>
> > wrote:
> >
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> >> Post images on http://www.imgur.com and include the link in your
> posting.
> >> *****
> >>
> >> Hi All,
> >>
> >> Does anyone know if there are standardized zstack image sets (with
> >> corresponding PSFs) available for testing deconvolution algorithms?
> >> Thanks!
> >>
> >> Best regards,
> >>
> >> Silas
> >>
> >> --
> >> Silas J. Leavesley, Ph.D.
> >> Professor
> >> Department of Chemical and Biomolecular Engineering
> >> Department of Pharmacology
> >> Center for Lung Biology
> >> University of South Alabama
> >> 150 Jaguar Drive, SH4129
> >> Mobile, AL 36688
> >> ph: (251)-460-6160
> >> fax: [phone]
> >> web: http://www.southalabama.edu/centers/bioimaging
> >>
> --
> Silas J. Leavesley, Ph.D.
> Professor
> Department of Chemical and Biomolecular Engineering
> Department of Pharmacology
> Center for Lung Biology
> University of South Alabama
> 150 Jaguar Drive, SH4129
> Mobile, AL 36688
> ph: (251)-460-6160
> fax: [phone]
> web: http://www.southalabama.edu/centers/bioimaging
>

--
Nathan O'Connor