reference z-corrections

[Kevin Braeckmans]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

 

Dear all,

 

For those interested, a rigorous treatment of how to correct for z-measurements in case of a mismatch in refractive indices can be found in the Handbook by Pawley, 3rd edition, chapter 20 by Egner and Hell. (I believe this chapter is also in the 2nd edition of the Handbook).

 

With regard to Esteban’s situation (see thread ‘How to correct z distance in RI mismatch’), yesterday I gave the suggestion to use the geometrical formula for an effective NA of approx. 1 (i.e. half the illumination light cone). Comparing this with the values reported in table 2 of the chapter by Egner and Esteban, a reasonable correspondence is found for a focus depth of 15 to 20 micron (less than a micron difference). After that the geometrical formula (with adjusted effective NA) does not give an adequate prediction anymore. In any case, in this chapter you can find everything needed for accurate calculations.

 

Best regards,

 

Kevin

 

Kevin Braeckmans, Ph.D.

Lab. General Biochemistry and Physical Pharmacy

Ghent University

Harelbekestraat 72

9000 Ghent

Belgium

Tel: [phone]

Fax: [phone]

[G. Esteban Fernandez]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Thanks for your persistence in finding a reference Kevin.  I read that
chapter in Pawley early on but didn't see any formulas that I could
quickly use to get numbers for my particular application.

One paper that presents z correction models that I was able to follow
and make an Excel spreadsheet for is:

van Elburg et al. (2007)  Improved correction of axial geometrical
distortion in index-mismatched fluorescent confocal microscopic images
using high-aperture objective lenses.  J. Microscopy 228(1):45-54.

They used "rigorous electromagnetic diffraction theory" to generate
numerical data (as in Egner and Hell's chapter in Pawley) and present
linear and non-linear models, trimmed down to relatively simple
equations, that fit the numbers.  They don't actually present the
rigours of the EM theory, so my mathematically simple mind wasn't
confused.  I don't have the expertise (or time!) to evaulate how good
their models are, but their equations in my spreadsheet churned out
numbers that agree with Table 20.2 and Fig. 20.10 in Pawley's book.
The corrected z-stacks gave results that my user says seem accurate.

If someone ever reads this post who knows more about the paper above
some feedback would be appreciated.

Esteban


On Feb 19, 2008 1:35 AM, Kevin Braeckmans <[hidden email]> wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>
>
>
> Dear all,
>
>
>
> For those interested, a rigorous treatment of how to correct for
> z-measurements in case of a mismatch in refractive indices can be found in
> the Handbook by Pawley, 3rd edition, chapter 20 by Egner and Hell. (I
> believe this chapter is also in the 2nd edition of the Handbook).
>
>
>
> With regard to Esteban's situation (see thread 'How to correct z distance in
> RI mismatch'), yesterday I gave the suggestion to use the geometrical
> formula for an effective NA of approx. 1 (i.e. half the illumination light
> cone). Comparing this with the values reported in table 2 of the chapter by
> Egner and Esteban, a reasonable correspondence is found for a focus depth of
> 15 to 20 micron (less than a micron difference). After that the geometrical
> formula (with adjusted effective NA) does not give an adequate prediction
> anymore. In any case, in this chapter you can find everything needed for
> accurate calculations.
>
>
>
> Best regards,
>
>
>
> Kevin
>
>
>
> Kevin Braeckmans, Ph.D.
>
> Lab. General Biochemistry and Physical Pharmacy
>
> Ghent University
>
> Harelbekestraat 72
>
> 9000 Ghent
>
> Belgium
>
> Tel: [phone]
>
> Fax: [phone]

--
G. Esteban Fernandez, Ph.D.
Associate Director
Molecular Cytology Research Core Facility
University of Missouri
1201 E. Rollins St.
Columbia, MO  65211

573-882-4895
573-884-9676 fax

http://www.biotech.missouri.edu/mcc/

[Csucs Gabor]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear All,

Again a non-confocal question: In order to check the functionality of
our incubator boxes we would like to purchase temperature and CO2
sensors which can be connected to a computer via USB (to perform
long-term measurements). Does anyone has experience (suggestions) with
such sensors?
>
Thanks     Gabor

--
Gabor Csucs
Light Microscopy Centre, ETH Zurich
Schafmattstrasse 18, HPM F16
CH-8093, Zurich, Switzerland

Web: www.lmc.ethz.ch
Phone: [phone]
Fax: [phone]
e-mail: [hidden email]

[Nuno Moreno]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I had never test it but I love the concept of the nova 5000.

http://www.fourier-sys.com/product_sensors_nova.html

Its a lovely toy that I'll buy for my kids when they grow up (for me to
play of course).

regards,
NM

Csucs Gabor wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Dear All,
>
> Again a non-confocal question: In order to check the functionality of
> our incubator boxes we would like to purchase temperature and CO2
> sensors which can be connected to a computer via USB (to perform
> long-term measurements). Does anyone has experience (suggestions) with
> such sensors?
>>
> Thanks     Gabor
>

--
Nuno Moreno
Cell Imaging Unit
Instituto Gulbenkian de Ciência
http://uic.igc.gulbekian.pt
http://www.igc.gulbekian.pt
phone [phone]
fax   [phone]

[Chris Tully]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Gabor,

I personally would start with Measurement Computing (http://www.measurementcomputing.com/).  They make a whole range of USB based DAQ (Data AQuisition) devices.  I have used some of their device in previous jobs.  I know that they have devices which accept RTD or thermocouple inputs for temperature, and they may well know of a CO2 sensor that you can use with their devices.

Chris Tully

On Feb 19, 2008 5:28 PM, Csucs Gabor <[hidden email]> wrote:

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear All,

Again a non-confocal question: In order to check the functionality of
our incubator boxes we would like to purchase temperature and CO2
sensors which can be connected to a computer via USB (to perform
long-term measurements). Does anyone has experience (suggestions) with
such sensors?
>
Thanks     Gabor

--
Gabor Csucs
Light Microscopy Centre, ETH Zurich
Schafmattstrasse 18, HPM F16
CH-8093, Zurich, Switzerland

Web: www.lmc.ethz.ch
Phone: [phone]
Fax: [phone]
e-mail: [hidden email]

[Caroline Bass]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

You might want to consider a data logger.  I have used thermochron
sensors, also known as ibuttons to measure core body temperature in
rodents.  But they are designed for use as monitoring devices.  You can
sterilize them, and you just set the button in the incubator and collect
the data whenever you need it.  Very flexible system, and it is super
cheap, as low as $5 a sensor and $30 some for the usb adaptor. They also
have wired solutions I believe.  I don't know about CO2 but they can
also keep track of humidity.


Check out the websites:

http://www.maxim-ic.com/products/ibutton/ibuttons/thermochron.cfm

and

http://www.maxim-ic.com/products/ibutton/


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Csucs Gabor
Sent: Tuesday, February 19, 2008 5:29 PM
To: [hidden email]
Subject: Temperature and CO2 sensors with USB connection

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear All,

Again a non-confocal question: In order to check the functionality of
our incubator boxes we would like to purchase temperature and CO2
sensors which can be connected to a computer via USB (to perform
long-term measurements). Does anyone has experience (suggestions) with
such sensors?
>
Thanks     Gabor

--
Gabor Csucs
Light Microscopy Centre, ETH Zurich
Schafmattstrasse 18, HPM F16
CH-8093, Zurich, Switzerland

Web: www.lmc.ethz.ch
Phone: [phone]
Fax: [phone]
e-mail: [hidden email]