Aberration correction

[Antonio Jose Pereira-2]

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Dear all,

I will test an Olympus objective on a Nikon Ti ...
I know that Olympus does all the chromatic aberration correction at the objective, but am unsure if Nikon distributes this correction between the objective and the tube lens. I would assume that the infinity path is already 'fully' corrected ... but would like to be sure. I appreciate any info on this.

Best,

Antonio Pereira
CID lab
i3S/IBMC, Universidade do Porto
Room 001.S2B, [phone] Ext. 6127

[PAVAK SHAH]

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Hi Antonio,

I have used Olympus objectives on a Zeiss body before (the 60x silicone oil
objective especially) and the mismatch causes chromatic aberration  that
results in a ~ 0.7 micron offset between ~green and ~red channels.
Depending on the application, this is straightforward to correct for using
multicolored beads and the SPIM registration plugin for Fiji by Stephan
Priebisch and may be worth the advantages of the particular objective you
want to use. Whether the degree of aberration will be similar on a Nikon
frame, I'm not sure but it should be easy to check.

Best,
Pavak

On Sat, Aug 1, 2020, 7:59 AM Antonio Jose Pereira <
[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.
> *****
>
> Dear all,
>
> I will test an Olympus objective on a Nikon Ti ...
> I know that Olympus does all the chromatic aberration correction at the
> objective, but am unsure if Nikon distributes this correction between the
> objective and the tube lens. I would assume that the infinity path is
> already 'fully' corrected ... but would like to be sure. I appreciate any
> info on this.
>
> Best,
>
> Antonio Pereira
> CID lab
> i3S/IBMC, Universidade do Porto
> Room 001.S2B, [phone] Ext. 6127
>

[George McNamara]

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Olympus, Nikon and Leica do all corrections in the objective lens.

Zeiss does some correction in tube lens.

George

p.s. in principle (maybe not in practice!) deconvolution software should
be able to correct aberrations.

p.p.s. deconvolution - Hari Shroff's lab and collaborators have a new
fast deconvolution paper, Guo et al 2020 Nature Biotechnology
https://www.nature.com/articles/s41587-020-0560-x with matlab/imagej
software and code in online supplement (text also mentions it posted to
github). Part of the abstract:

"Here we describe theoretical and practical advances in algorithm and
software design that result in image processing times that are tenfold
to several thousand fold faster than with previous methods. First, we
show that an ‘unmatched back projector’ accelerates deconvolution
relative to the classic Richardson–Lucy algorithm by at least tenfold.
Second, three-dimensional image-based registration with a graphics
processing unit enhances processing speed 10- to 100-fold over CPU
processing."

On 8/1/2020 10:58 AM, Antonio Jose Pereira 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.
> *****
>
> Dear all,
>
> I will test an Olympus objective on a Nikon Ti ...
> I know that Olympus does all the chromatic aberration correction at the objective, but am unsure if Nikon distributes this correction between the objective and the tube lens. I would assume that the infinity path is already 'fully' corrected ... but would like to be sure. I appreciate any info on this.
>
> Best,
>
> Antonio Pereira
> CID lab
> i3S/IBMC, Universidade do Porto
> Room 001.S2B, [phone] Ext. 6127

[Craig Brideau]

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I've heard that Leica does a bit of correction on the violet end in the
tube lens, but have not verified personally. Zeiss does quite a bit of
correction in its tube lens design so you should only use Zeiss with Zeiss.
I have interchanged Nikon and Olympus freely without major issue, although
since Olympus is designed for a 180mm tube lens and Nikon for 200mm, your
field and magnification will be slightly different than usual.

Craig

On Sat, Aug 1, 2020 at 9:59 AM George McNamara <[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.
> *****
>
> Olympus, Nikon and Leica do all corrections in the objective lens.
>
> Zeiss does some correction in tube lens.
>
> George
>
> p.s. in principle (maybe not in practice!) deconvolution software should
> be able to correct aberrations.
>
> p.p.s. deconvolution - Hari Shroff's lab and collaborators have a new
> fast deconvolution paper, Guo et al 2020 Nature Biotechnology
> https://www.nature.com/articles/s41587-020-0560-x with matlab/imagej
> software and code in online supplement (text also mentions it posted to
> github). Part of the abstract:
>
> "Here we describe theoretical and practical advances in algorithm and
> software design that result in image processing times that are tenfold
> to several thousand fold faster than with previous methods. First, we
> show that an ‘unmatched back projector’ accelerates deconvolution
> relative to the classic Richardson–Lucy algorithm by at least tenfold.
> Second, three-dimensional image-based registration with a graphics
> processing unit enhances processing speed 10- to 100-fold over CPU
> processing."
>
> On 8/1/2020 10:58 AM, Antonio Jose Pereira 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.
> > *****
> >
> > Dear all,
> >
> > I will test an Olympus objective on a Nikon Ti ...
> > I know that Olympus does all the chromatic aberration correction at the
> objective, but am unsure if Nikon distributes this correction between the
> objective and the tube lens. I would assume that the infinity path is
> already 'fully' corrected ... but would like to be sure. I appreciate any
> info on this.
> >
> > Best,
> >
> > Antonio Pereira
> > CID lab
> > i3S/IBMC, Universidade do Porto
> > Room 001.S2B, [phone] Ext. 6127
>

[Marc Reinig-2]

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*****

Aside from chromatic distortion, do any of the manufacturers do
compensation in the tube lens for other aberrations?

Marco

On Sat, Aug 1, 2020 at 11:02 Craig Brideau <[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.
> *****
>
> I've heard that Leica does a bit of correction on the violet end in the
> tube lens, but have not verified personally. Zeiss does quite a bit of
> correction in its tube lens design so you should only use Zeiss with Zeiss.
> I have interchanged Nikon and Olympus freely without major issue, although
> since Olympus is designed for a 180mm tube lens and Nikon for 200mm, your
> field and magnification will be slightly different than usual.
>
> Craig
>
> On Sat, Aug 1, 2020 at 9:59 AM George McNamara <[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.
> > *****
> >
> > Olympus, Nikon and Leica do all corrections in the objective lens.
> >
> > Zeiss does some correction in tube lens.
> >
> > George
> >
> > p.s. in principle (maybe not in practice!) deconvolution software should
> > be able to correct aberrations.
> >
> > p.p.s. deconvolution - Hari Shroff's lab and collaborators have a new
> > fast deconvolution paper, Guo et al 2020 Nature Biotechnology
> > https://www.nature.com/articles/s41587-020-0560-x with matlab/imagej
> > software and code in online supplement (text also mentions it posted to
> > github). Part of the abstract:
> >
> > "Here we describe theoretical and practical advances in algorithm and
> > software design that result in image processing times that are tenfold
> > to several thousand fold faster than with previous methods. First, we
> > show that an ‘unmatched back projector’ accelerates deconvolution
> > relative to the classic Richardson–Lucy algorithm by at least tenfold.
> > Second, three-dimensional image-based registration with a graphics
> > processing unit enhances processing speed 10- to 100-fold over CPU
> > processing."
> >
> > On 8/1/2020 10:58 AM, Antonio Jose Pereira 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.
> > > *****
> > >
> > > Dear all,
> > >
> > > I will test an Olympus objective on a Nikon Ti ...
> > > I know that Olympus does all the chromatic aberration correction at the
> > objective, but am unsure if Nikon distributes this correction between the
> > objective and the tube lens. I would assume that the infinity path is
> > already 'fully' corrected ... but would like to be sure. I appreciate any
> > info on this.
> > >
> > > Best,
> > >
> > > Antonio Pereira
> > > CID lab
> > > i3S/IBMC, Universidade do Porto
> > > Room 001.S2B, [phone] Ext. 6127
> >
>

--
Marco

Sent from my iPhone

[Antonio Jose Pereira-2]

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*****

Great. Thank you all. The question is answered.

Now I wonder why some companies choose to split the correction between the objective and the tube lens. Unless the achieved performance gains from the splitting, we'll then have an infinity path segment which is sub-optimal for injection of e.g. ultra-short pulses. If I'm thinking correctly, the infinity segment is then only 'infinite' at some spectral points after all.

Thanks,
Antonio

----- Original Message -----
From: "Craig Brideau" <[hidden email]>
To: "CONFOCALMICROSCOPY" <[hidden email]>
Sent: Saturday, 1 August, 2020 18:56:35
Subject: Re: Aberration correction

*****
To join, leave or search the confocal microscopy listserv, go to:
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*****

I've heard that Leica does a bit of correction on the violet end in the
tube lens, but have not verified personally. Zeiss does quite a bit of
correction in its tube lens design so you should only use Zeiss with Zeiss.
I have interchanged Nikon and Olympus freely without major issue, although
since Olympus is designed for a 180mm tube lens and Nikon for 200mm, your
field and magnification will be slightly different than usual.

Craig

On Sat, Aug 1, 2020 at 9:59 AM George McNamara <[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.
> *****
>
> Olympus, Nikon and Leica do all corrections in the objective lens.
>
> Zeiss does some correction in tube lens.
>
> George
>
> p.s. in principle (maybe not in practice!) deconvolution software should
> be able to correct aberrations.
>
> p.p.s. deconvolution - Hari Shroff's lab and collaborators have a new
> fast deconvolution paper, Guo et al 2020 Nature Biotechnology
> https://www.nature.com/articles/s41587-020-0560-x with matlab/imagej
> software and code in online supplement (text also mentions it posted to
> github). Part of the abstract:
>
> "Here we describe theoretical and practical advances in algorithm and
> software design that result in image processing times that are tenfold
> to several thousand fold faster than with previous methods. First, we
> show that an ‘unmatched back projector’ accelerates deconvolution
> relative to the classic Richardson–Lucy algorithm by at least tenfold.
> Second, three-dimensional image-based registration with a graphics
> processing unit enhances processing speed 10- to 100-fold over CPU
> processing."
>
> On 8/1/2020 10:58 AM, Antonio Jose Pereira 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.
> > *****
> >
> > Dear all,
> >
> > I will test an Olympus objective on a Nikon Ti ...
> > I know that Olympus does all the chromatic aberration correction at the
> objective, but am unsure if Nikon distributes this correction between the
> objective and the tube lens. I would assume that the infinity path is
> already 'fully' corrected ... but would like to be sure. I appreciate any
> info on this.
> >
> > Best,
> >
> > Antonio Pereira
> > CID lab
> > i3S/IBMC, Universidade do Porto
> > Room 001.S2B, [phone] Ext. 6127
>

[Marc Reinig-2]

*****
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.
*****

You can pre-compensate the laser beam to counter the characteristics of the
lens/system.

Marco

On Sat, Aug 1, 2020 at 12:59 Antonio Jose Pereira <
[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.
> *****
>
> Great. Thank you all. The question is answered.
>
> Now I wonder why some companies choose to split the correction between the
> objective and the tube lens. Unless the achieved performance gains from the
> splitting, we'll then have an infinity path segment which is sub-optimal
> for injection of e.g. ultra-short pulses. If I'm thinking correctly, the
> infinity segment is then only 'infinite' at some spectral points after all.
>
> Thanks,
> Antonio
>
> ----- Original Message -----
> From: "Craig Brideau" <[hidden email]>
> To: "CONFOCALMICROSCOPY" <[hidden email]>
> Sent: Saturday, 1 August, 2020 18:56:35
> Subject: Re: Aberration correction
>
> *****
> 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.
> *****
>
> I've heard that Leica does a bit of correction on the violet end in the
> tube lens, but have not verified personally. Zeiss does quite a bit of
> correction in its tube lens design so you should only use Zeiss with Zeiss.
> I have interchanged Nikon and Olympus freely without major issue, although
> since Olympus is designed for a 180mm tube lens and Nikon for 200mm, your
> field and magnification will be slightly different than usual.
>
> Craig
>
> On Sat, Aug 1, 2020 at 9:59 AM George McNamara <[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.
> > *****
> >
> > Olympus, Nikon and Leica do all corrections in the objective lens.
> >
> > Zeiss does some correction in tube lens.
> >
> > George
> >
> > p.s. in principle (maybe not in practice!) deconvolution software should
> > be able to correct aberrations.
> >
> > p.p.s. deconvolution - Hari Shroff's lab and collaborators have a new
> > fast deconvolution paper, Guo et al 2020 Nature Biotechnology
> > https://www.nature.com/articles/s41587-020-0560-x with matlab/imagej
> > software and code in online supplement (text also mentions it posted to
> > github). Part of the abstract:
> >
> > "Here we describe theoretical and practical advances in algorithm and
> > software design that result in image processing times that are tenfold
> > to several thousand fold faster than with previous methods. First, we
> > show that an ‘unmatched back projector’ accelerates deconvolution
> > relative to the classic Richardson–Lucy algorithm by at least tenfold.
> > Second, three-dimensional image-based registration with a graphics
> > processing unit enhances processing speed 10- to 100-fold over CPU
> > processing."
> >
> > On 8/1/2020 10:58 AM, Antonio Jose Pereira 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.
> > > *****
> > >
> > > Dear all,
> > >
> > > I will test an Olympus objective on a Nikon Ti ...
> > > I know that Olympus does all the chromatic aberration correction at the
> > objective, but am unsure if Nikon distributes this correction between the
> > objective and the tube lens. I would assume that the infinity path is
> > already 'fully' corrected ... but would like to be sure. I appreciate any
> > info on this.
> > >
> > > Best,
> > >
> > > Antonio Pereira
> > > CID lab
> > > i3S/IBMC, Universidade do Porto
> > > Room 001.S2B, [phone] Ext. 6127
> >
>

--
Marco

Sent from my iPhone

[Benjamin Smith]

*****
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*****

Without having an actual model of the lenses it is hard to say for certain,
but I can say from personal experience in engineering optical systems, it
is very hard and expensive to have a fully corrected single optical
element, especially one that works across the broad array of wavelengths
and resolutions encountered on a microscope. The moment you fix one
aberration, you exacerbate another as everything is kind of
interdependent.  Therefore, quite often it is much easier to get things
close to perfect within each lens system of the microscope, and then simply
ensure that the slight remaining aberrations within each lens system have
opposite signs completing the correction across a wider array of
wavelengths.

For example, even with something as simple as an achromatic Gallilean beam
expander, you will run into this lens-pair dependent effect.   Even though
as a stand-alone lens, you will find that most vendor's lenses tend to
perform close to one another, they will all have different
residual aberrations (due to different design wavelengths, glass
formulation/thickness, etc.).  Therefore, by carefully combining the right
lens pair such that the signs of their residual aberrations are opposite
one another, you can get your optical system to well out-perform the specs
on either individual component.  As such, since the microscope
manufacturers know the composition and residual aberrations of their own
optical systems, they have the advantage of making the objective and tube
lens complimentary in this way to further increase the performance above
that of just the objective or tube lens alone (or at least ensure the
residual aberrations are not additive).  Not saying this is what they do,
but it would definitely make sense if they did.  This would also mean that
mixing and matching could lead to additive residual aberrations making the
system underperform, although this underperformance should be slight, since
the objective and tube lens are already extensively corrected on their own.

-Ben Smith

On Sat, Aug 1, 2020 at 1:04 PM Marc Reinig <[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.
> *****
>
> You can pre-compensate the laser beam to counter the characteristics of the
> lens/system.
>
> Marco
>
> On Sat, Aug 1, 2020 at 12:59 Antonio Jose Pereira <
> [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.
> > *****
> >
> > Great. Thank you all. The question is answered.
> >
> > Now I wonder why some companies choose to split the correction between
> the
> > objective and the tube lens. Unless the achieved performance gains from
> the
> > splitting, we'll then have an infinity path segment which is sub-optimal
> > for injection of e.g. ultra-short pulses. If I'm thinking correctly, the
> > infinity segment is then only 'infinite' at some spectral points after
> all.
> >
> > Thanks,
> > Antonio
> >
> > ----- Original Message -----
> > From: "Craig Brideau" <[hidden email]>
> > To: "CONFOCALMICROSCOPY" <[hidden email]>
> > Sent: Saturday, 1 August, 2020 18:56:35
> > Subject: Re: Aberration correction
> >
> > *****
> > 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.
> > *****
> >
> > I've heard that Leica does a bit of correction on the violet end in the
> > tube lens, but have not verified personally. Zeiss does quite a bit of
> > correction in its tube lens design so you should only use Zeiss with
> Zeiss.
> > I have interchanged Nikon and Olympus freely without major issue,
> although
> > since Olympus is designed for a 180mm tube lens and Nikon for 200mm, your
> > field and magnification will be slightly different than usual.
> >
> > Craig
> >
> > On Sat, Aug 1, 2020 at 9:59 AM George McNamara <
> [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.
> > > *****
> > >
> > > Olympus, Nikon and Leica do all corrections in the objective lens.
> > >
> > > Zeiss does some correction in tube lens.
> > >
> > > George
> > >
> > > p.s. in principle (maybe not in practice!) deconvolution software
> should
> > > be able to correct aberrations.
> > >
> > > p.p.s. deconvolution - Hari Shroff's lab and collaborators have a new
> > > fast deconvolution paper, Guo et al 2020 Nature Biotechnology
> > > https://www.nature.com/articles/s41587-020-0560-x with matlab/imagej
> > > software and code in online supplement (text also mentions it posted to
> > > github). Part of the abstract:
> > >
> > > "Here we describe theoretical and practical advances in algorithm and
> > > software design that result in image processing times that are tenfold
> > > to several thousand fold faster than with previous methods. First, we
> > > show that an ‘unmatched back projector’ accelerates deconvolution
> > > relative to the classic Richardson–Lucy algorithm by at least tenfold.
> > > Second, three-dimensional image-based registration with a graphics
> > > processing unit enhances processing speed 10- to 100-fold over CPU
> > > processing."
> > >
> > > On 8/1/2020 10:58 AM, Antonio Jose Pereira 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.
> > > > *****
> > > >
> > > > Dear all,
> > > >
> > > > I will test an Olympus objective on a Nikon Ti ...
> > > > I know that Olympus does all the chromatic aberration correction at
> the
> > > objective, but am unsure if Nikon distributes this correction between
> the
> > > objective and the tube lens. I would assume that the infinity path is
> > > already 'fully' corrected ... but would like to be sure. I appreciate
> any
> > > info on this.
> > > >
> > > > Best,
> > > >
> > > > Antonio Pereira
> > > > CID lab
> > > > i3S/IBMC, Universidade do Porto
> > > > Room 001.S2B, [phone] Ext. 6127
> > >
> >
> --
> Marco
>
> Sent from my iPhone
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Life Sciences Addition
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/

[Ciaran Butler-Hallissey]

*****
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*****

Has anyone ever been routinely provided (or asked vendors) for ranges of "reasonable" chromatic abberation per objective?

For instance, after installation or service when a system is aligned correctly.

Best,

Ciaran

Cell Imaging and Cytometry,
Turku Bioscience,
Website: https://bioscience.fi/cic