Settings adjustment with depth for a Zeiss LSM 510

[Pedro Almada]

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Dear listers,

Does anyone know of a VBA macro for the Zeiss Meta which allows users to
adjust settings such as gain and laser power according to current focus for
the Zeiss LSM 510? I am interested in developing this myself but if there is
something already made, that would be great...

If you are curious what it's for, it's for some of our users who image whole
drosophila brains for structural information. Their common complaint is that
half-way through their z-stack they loose image brightness until the last
slices are barely visible. Clearing methods like Methyl salicilate aren't
really adequate for neuronal structure I'm told, which leads me to consider
this method.

Either way, any information is welcome.

Thanks for reading,
Cheers,
Pedro Almada
*
*
Research and Microscopy Technician
Unidade de Imagiologia Celular,
*Instituto Gulbenkian de Ciência*
Rua da Quinta Grande, 6
2780-156 Oeiras

Phone: + 351 214 464 607
Ext: 607

[Martin Wessendorf-2]

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Dear Pedro--

On 7/26/2011 9:26 AM, Pedro Almada wrote:

> If you are curious what it's for, it's for some of our users who image whole
> drosophila brains for structural information. Their common complaint is that
> half-way through their z-stack they loose image brightness until the last
> slices are barely visible. Clearing methods like Methyl salicilate aren't
> really adequate for neuronal structure I'm told, which leads me to consider
> this method.

This is a long shot, but is there any chance that they're over-staining
their tissue?  If they're using high concentrations of their
fluorophores, they may be absorbing most of the light in the top half of
the tissue, leaving no photons for the bottom half.  Cutting back the
concentration of secondary antibodies would be expected to improve
penetration, if this were the case.

Good luck!

Martin Wessendorf

--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455                    e-mail: [hidden email]

[G. Esteban Fernandez]

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The acquisition software (LSM or ZEN) has that function built in, no need
for a macro.  It is called something like "Z brightness correction" and is
in the Z stack panel.

Software manuals for LSM and ZEN can be found at the Zeiss FTP site here:
ftp://lsm.zeiss.com/LSM/User_Area/Manuals/

-Esteban

On Tue, Jul 26, 2011 at 7:26 AM, Pedro Almada <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear listers,
>
> Does anyone know of a VBA macro for the Zeiss Meta which allows users to
> adjust settings such as gain and laser power according to current focus for
> the Zeiss LSM 510? I am interested in developing this myself but if there
> is
> something already made, that would be great...
>
> If you are curious what it's for, it's for some of our users who image
> whole
> drosophila brains for structural information. Their common complaint is
> that
> half-way through their z-stack they loose image brightness until the last
> slices are barely visible. Clearing methods like Methyl salicilate aren't
> really adequate for neuronal structure I'm told, which leads me to consider
> this method.
>
> Either way, any information is welcome.
>
> Thanks for reading,
> Cheers,
> Pedro Almada
> *
> *
> Research and Microscopy Technician
> Unidade de Imagiologia Celular,
> *Instituto Gulbenkian de Ciência*
> Rua da Quinta Grande, 6
> 2780-156 Oeiras
>
> Phone: + 351 214 464 607
> Ext: 607

[Pedro Almada]

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

Hi Esteban and Martin,

Thanks alot for the help. I admit I wasn't aware of the option being in the
software itself. I'll try and have a look at their preparations myself and
check for oversaturation (if I remember their pictures correctly, that
sounds like a definite possibility).

Thanks again, this is a very helpful and interesting list.

All the best,
Pedro

On 26 July 2011 16:37, G. Esteban Fernandez
<[hidden email]>wrote:

> The acquisition software (LSM or ZEN) has that function built in, no need
> for a macro.  It is called something like "Z brightness correction" and is
> in the Z stack panel.
>
> Software manuals for LSM and ZEN can be found at the Zeiss FTP site here:
> ftp://lsm.zeiss.com/LSM/User_Area/Manuals/
>
> -Esteban
>
> On Tue, Jul 26, 2011 at 7:26 AM, Pedro Almada <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Dear listers,
>>
>> Does anyone know of a VBA macro for the Zeiss Meta which allows users to
>> adjust settings such as gain and laser power according to current focus
>> for
>> the Zeiss LSM 510? I am interested in developing this myself but if there
>> is
>> something already made, that would be great...
>>
>> If you are curious what it's for, it's for some of our users who image
>> whole
>> drosophila brains for structural information. Their common complaint is
>> that
>> half-way through their z-stack they loose image brightness until the last
>> slices are barely visible. Clearing methods like Methyl salicilate aren't
>> really adequate for neuronal structure I'm told, which leads me to
>> consider
>> this method.
>>
>> Either way, any information is welcome.
>>
>> Thanks for reading,
>> Cheers,
>> Pedro Almada
>> *
>> *
>> Research and Microscopy Technician
>> Unidade de Imagiologia Celular,
>> *Instituto Gulbenkian de Ciência*
>> Rua da Quinta Grande, 6
>> 2780-156 Oeiras
>>
>> Phone: + 351 214 464 607
>> Ext: 607
>>
>

[Jacqueline Ross]

Hi Pedro,

We also have an LSM 510 META. If you have the Guided Tour PDF, page 45 explains how to use the Auto Z Brightness correction. However, you can only set 2 positions (with associated gain/offset) so sometimes this isn't enough.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Pedro Almada
Sent: Wednesday, 27 July 2011 10:25 p.m.
To: [hidden email]
Subject: Re: Settings adjustment with depth for a Zeiss LSM 510

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

Hi Esteban and Martin,

Thanks alot for the help. I admit I wasn't aware of the option being in the
software itself. I'll try and have a look at their preparations myself and
check for oversaturation (if I remember their pictures correctly, that
sounds like a definite possibility).

Thanks again, this is a very helpful and interesting list.

All the best,
Pedro

On 26 July 2011 16:37, G. Esteban Fernandez
<[hidden email]>wrote:

> The acquisition software (LSM or ZEN) has that function built in, no need
> for a macro.  It is called something like "Z brightness correction" and is
> in the Z stack panel.
>
> Software manuals for LSM and ZEN can be found at the Zeiss FTP site here:
> ftp://lsm.zeiss.com/LSM/User_Area/Manuals/
>
> -Esteban
>
> On Tue, Jul 26, 2011 at 7:26 AM, Pedro Almada <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Dear listers,
>>
>> Does anyone know of a VBA macro for the Zeiss Meta which allows users to
>> adjust settings such as gain and laser power according to current focus
>> for
>> the Zeiss LSM 510? I am interested in developing this myself but if there
>> is
>> something already made, that would be great...
>>
>> If you are curious what it's for, it's for some of our users who image
>> whole
>> drosophila brains for structural information. Their common complaint is
>> that
>> half-way through their z-stack they loose image brightness until the last
>> slices are barely visible. Clearing methods like Methyl salicilate aren't
>> really adequate for neuronal structure I'm told, which leads me to
>> consider
>> this method.
>>
>> Either way, any information is welcome.
>>
>> Thanks for reading,
>> Cheers,
>> Pedro Almada
>> *
>> *
>> Research and Microscopy Technician
>> Unidade de Imagiologia Celular,
>> *Instituto Gulbenkian de Ciência*
>> Rua da Quinta Grande, 6
>> 2780-156 Oeiras
>>
>> Phone: + 351 214 464 607
>> Ext: 607
>>
>

[G. Esteban Fernandez]

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

In case it's useful enough to you to warrant an upgrade, the new Zeiss
confocal software, ZEN, allows more than two set points plus variable laser
power in addition to variable detector settings.  (No commercial interest)

-Esteban




On Wed, Jul 27, 2011 at 5:55 PM, Jacqui Ross <[hidden email]>wrote:

> Hi Pedro,
>
> We also have an LSM 510 META. If you have the Guided Tour PDF, page 45
> explains how to use the Auto Z Brightness correction. However, you can only
> set 2 positions (with associated gain/offset) so sometimes this isn't
> enough.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Pedro Almada
> Sent: Wednesday, 27 July 2011 10:25 p.m.
> To: [hidden email]
> Subject: Re: Settings adjustment with depth for a Zeiss LSM 510
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Esteban and Martin,
>
> Thanks alot for the help. I admit I wasn't aware of the option being in the
> software itself. I'll try and have a look at their preparations myself and
> check for oversaturation (if I remember their pictures correctly, that
> sounds like a definite possibility).
>
> Thanks again, this is a very helpful and interesting list.
>
> All the best,
> Pedro
>
> On 26 July 2011 16:37, G. Esteban Fernandez
> <[hidden email]>wrote:
>
> > The acquisition software (LSM or ZEN) has that function built in, no need
> > for a macro.  It is called something like "Z brightness correction" and
> is
> > in the Z stack panel.
> >
> > Software manuals for LSM and ZEN can be found at the Zeiss FTP site here:
> > ftp://lsm.zeiss.com/LSM/User_Area/Manuals/
> >
> > -Esteban
> >
> > On Tue, Jul 26, 2011 at 7:26 AM, Pedro Almada <[hidden email]> wrote:
> >
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> >> *****
> >>
> >> Dear listers,
> >>
> >> Does anyone know of a VBA macro for the Zeiss Meta which allows users to
> >> adjust settings such as gain and laser power according to current focus
> >> for
> >> the Zeiss LSM 510? I am interested in developing this myself but if
> there
> >> is
> >> something already made, that would be great...
> >>
> >> If you are curious what it's for, it's for some of our users who image
> >> whole
> >> drosophila brains for structural information. Their common complaint is
> >> that
> >> half-way through their z-stack they loose image brightness until the
> last
> >> slices are barely visible. Clearing methods like Methyl salicilate
> aren't
> >> really adequate for neuronal structure I'm told, which leads me to
> >> consider
> >> this method.
> >>
> >> Either way, any information is welcome.
> >>
> >> Thanks for reading,
> >> Cheers,
> >> Pedro Almada
> >> *
> >> *
> >> Research and Microscopy Technician
> >> Unidade de Imagiologia Celular,
> >> *Instituto Gulbenkian de Ciência*
> >> Rua da Quinta Grande, 6
> >> 2780-156 Oeiras
> >>
> >> Phone: + 351 214 464 607
> >> Ext: 607
> >>
> >
>

[shaohuih]

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

We have a Zeiss 510 Meta, and would like to learn more its software too.  However, the Zeiss FTP site listed below requires an Username and Password.  How can we access the FTP site?

Shaohui Huang, Ph.D.
Institute for Environmental Medicine
UPenn School of Medicine

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Jacqui Ross
Sent: Wednesday, July 27, 2011 8:56 PM
To: [hidden email]
Subject: Re: Settings adjustment with depth for a Zeiss LSM 510

Hi Pedro,

We also have an LSM 510 META. If you have the Guided Tour PDF, page 45 explains how to use the Auto Z Brightness correction. However, you can only set 2 positions (with associated gain/offset) so sometimes this isn't enough.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Pedro Almada
Sent: Wednesday, 27 July 2011 10:25 p.m.
To: [hidden email]
Subject: Re: Settings adjustment with depth for a Zeiss LSM 510

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

Hi Esteban and Martin,

Thanks alot for the help. I admit I wasn't aware of the option being in the software itself. I'll try and have a look at their preparations myself and check for oversaturation (if I remember their pictures correctly, that sounds like a definite possibility).

Thanks again, this is a very helpful and interesting list.

All the best,
Pedro

On 26 July 2011 16:37, G. Esteban Fernandez
<[hidden email]>wrote:

> The acquisition software (LSM or ZEN) has that function built in, no
> need for a macro.  It is called something like "Z brightness
> correction" and is in the Z stack panel.
>
> Software manuals for LSM and ZEN can be found at the Zeiss FTP site here:
> ftp://lsm.zeiss.com/LSM/User_Area/Manuals/
>
> -Esteban
>
> On Tue, Jul 26, 2011 at 7:26 AM, Pedro Almada <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Dear listers,
>>
>> Does anyone know of a VBA macro for the Zeiss Meta which allows users
>> to adjust settings such as gain and laser power according to current
>> focus for the Zeiss LSM 510? I am interested in developing this
>> myself but if there is something already made, that would be great...
>>
>> If you are curious what it's for, it's for some of our users who
>> image whole drosophila brains for structural information. Their
>> common complaint is that half-way through their z-stack they loose
>> image brightness until the last slices are barely visible. Clearing
>> methods like Methyl salicilate aren't really adequate for neuronal
>> structure I'm told, which leads me to consider this method.
>>
>> Either way, any information is welcome.
>>
>> Thanks for reading,
>> Cheers,
>> Pedro Almada
>> *
>> *
>> Research and Microscopy Technician
>> Unidade de Imagiologia Celular,
>> *Instituto Gulbenkian de Ciência*
>> Rua da Quinta Grande, 6
>> 2780-156 Oeiras
>>
>> Phone: + 351 214 464 607
>> Ext: 607
>>
>

[G. Esteban Fernandez]

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

Username is instrument serial number, password is dongle number (software
license number), should be on USB stick on back of computer.  If that
doesn't work call your local Zeiss rep. or support at 800-233-2343.

-Esteban

On Tue, Aug 2, 2011 at 10:21 AM, Jack Huang <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We have a Zeiss 510 Meta, and would like to learn more its software too.
>  However, the Zeiss FTP site listed below requires an Username and Password.
>  How can we access the FTP site?
>
> Shaohui Huang, Ph.D.
> Institute for Environmental Medicine
> UPenn School of Medicine
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Jacqui Ross
> Sent: Wednesday, July 27, 2011 8:56 PM
> To: [hidden email]
> Subject: Re: Settings adjustment with depth for a Zeiss LSM 510
>
> Hi Pedro,
>
> We also have an LSM 510 META. If you have the Guided Tour PDF, page 45
> explains how to use the Auto Z Brightness correction. However, you can only
> set 2 positions (with associated gain/offset) so sometimes this isn't
> enough.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Pedro Almada
> Sent: Wednesday, 27 July 2011 10:25 p.m.
> To: [hidden email]
> Subject: Re: Settings adjustment with depth for a Zeiss LSM 510
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Esteban and Martin,
>
> Thanks alot for the help. I admit I wasn't aware of the option being in the
> software itself. I'll try and have a look at their preparations myself and
> check for oversaturation (if I remember their pictures correctly, that
> sounds like a definite possibility).
>
> Thanks again, this is a very helpful and interesting list.
>
> All the best,
> Pedro
>
> On 26 July 2011 16:37, G. Esteban Fernandez
> <[hidden email]>wrote:
>
> > The acquisition software (LSM or ZEN) has that function built in, no
> > need for a macro.  It is called something like "Z brightness
> > correction" and is in the Z stack panel.
> >
> > Software manuals for LSM and ZEN can be found at the Zeiss FTP site here:
> > ftp://lsm.zeiss.com/LSM/User_Area/Manuals/
> >
> > -Esteban
> >
> > On Tue, Jul 26, 2011 at 7:26 AM, Pedro Almada <[hidden email]> wrote:
> >
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> >> *****
> >>
> >> Dear listers,
> >>
> >> Does anyone know of a VBA macro for the Zeiss Meta which allows users
> >> to adjust settings such as gain and laser power according to current
> >> focus for the Zeiss LSM 510? I am interested in developing this
> >> myself but if there is something already made, that would be great...
> >>
> >> If you are curious what it's for, it's for some of our users who
> >> image whole drosophila brains for structural information. Their
> >> common complaint is that half-way through their z-stack they loose
> >> image brightness until the last slices are barely visible. Clearing
> >> methods like Methyl salicilate aren't really adequate for neuronal
> >> structure I'm told, which leads me to consider this method.
> >>
> >> Either way, any information is welcome.
> >>
> >> Thanks for reading,
> >> Cheers,
> >> Pedro Almada
> >> *
> >> *
> >> Research and Microscopy Technician
> >> Unidade de Imagiologia Celular,
> >> *Instituto Gulbenkian de Ciência*
> >> Rua da Quinta Grande, 6
> >> 2780-156 Oeiras
> >>
> >> Phone: + 351 214 464 607
> >> Ext: 607
> >>
> >
>