Source of Richardson test slide

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Shalin Mehta Shalin Mehta
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Source of Richardson test slide

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

 Does anyone has recommendations on from where to by a transparent Richardson test slide for phase imaging? I have found couple of companies with google and also some pages of researchers that suggest that very few companies provide well calibrated slides. The original manufacturer's website: www.richardson-tech.com is down.

Thanks in advance for inputs
shalin

--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm
Barbara Foster Barbara Foster
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Re: Source of Richardson test slide

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

Unfortunately, Richardson has gone out of business.  You might try EMS Diatome.  They were one of Richardson's strongest supporters.

Good hunting,
Barbara

At 04:50 PM 6/18/2008, you wrote:
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All,

 Does anyone has recommendations on from where to by a transparent Richardson test slide for phase imaging? I have found couple of companies with google and also some pages of researchers that suggest that very few companies provide well calibrated slides. The original manufacturer's website: www.richardson-tech.com is down.

Thanks in advance for inputs
shalin

--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm
Shalin Mehta Shalin Mehta
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Re: Source of Richardson test slide

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara,
 EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email.
Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells.
btw folks, pardon the 'blurred' English in last mail.

cheers
Shalin

On Thu, Jun 19, 2008 at 9:23 PM, Barbara Foster <[hidden email]> wrote:
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Hi, Shalin

Unfortunately, Richardson has gone out of business.  You might try EMS Diatome.  They were one of Richardson's strongest supporters.

Good hunting,
Barbara

At 04:50 PM 6/18/2008, you wrote:
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All,


 Does anyone has recommendations on from where to by a transparent Richardson test slide for phase imaging? I have found couple of companies with google and also some pages of researchers that suggest that very few companies provide well calibrated slides. The original manufacturer's website: www.richardson-tech.com is down.

Thanks in advance for inputs
shalin

--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm



--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm
Sam's Mail Sam's Mail
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Re: Source of Richardson test slide. .

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

Why not use the everpresent molecular probes test slides?  FluoCells prepared slide #3 would be a likely candidate.  I use it for fluorescent and DIC alignment checks often.  It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs.  Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too.
--
Samuel A. Connell
Director of Light Microscopy
Cell & Tissue Imaging Center
St. Jude Children's Research Hospital
332 North Lauderdale St., E7061
Memphis, TN 38105-2794
(901) 495-2536
[hidden email]


________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Shalin Mehta [[hidden email]]
Sent: Thursday, June 19, 2008 7:47 PM
To: [hidden email]
Subject: Re: Source of Richardson test slide.    .

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara,
 EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email.
Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells.
btw folks, pardon the 'blurred' English in last mail.

cheers
Shalin

On Thu, Jun 19, 2008 at 9:23 PM, Barbara Foster <[hidden email]<mailto:[hidden email]>> wrote:
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Hi, Shalin

Unfortunately, Richardson has gone out of business.  You might try EMS Diatome.  They were one of Richardson's strongest supporters.

Good hunting,
Barbara

At 04:50 PM 6/18/2008, you wrote:
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Dear All,


 Does anyone has recommendations on from where to by a transparent Richardson test slide for phase imaging? I have found couple of companies with google and also some pages of researchers that suggest that very few companies provide well calibrated slides. The original manufacturer's website: www.richardson-tech.com<http://www.richardson-tech.com> is down.

Thanks in advance for inputs
shalin

--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com<http://shalin.wordpress.com>
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm



--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com<http://shalin.wordpress.com>
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm
Shalin Mehta Shalin Mehta
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Re: Source of Richardson test slide. .

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have clarified. I am working on a method for imaging cell cultures on plastic in bas-relief. At the risk of self-promotion, I am posting link to the recent conference presentation: http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf

We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells.

cheers
shalin



On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote:
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Why not use the everpresent molecular probes test slides?  FluoCells prepared slide #3 would be a likely candidate.  I use it for fluorescent and DIC alignment checks often.  It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs.  Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too.
--
Samuel A. Connell
Director of Light Microscopy
Cell & Tissue Imaging Center
St. Jude Children's Research Hospital
332 North Lauderdale St., E7061
Memphis, TN 38105-2794
(901) 495-2536
[hidden email]


________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Shalin Mehta [[hidden email]]
Sent: Thursday, June 19, 2008 7:47 PM
To: [hidden email]
Subject: Re: Source of Richardson test slide.    .

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara,
 EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email.
Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells.
btw folks, pardon the 'blurred' English in last mail.

cheers
Shalin

James Pawley James Pawley
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Re: Source of Richardson test slide. .

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Re: Source of Richardson test slide. .
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have clarified. I am working on a method for imaging cell cultures on plastic in bas-relief. At the risk of self-promotion, I am posting link to the recent conference presentation: http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf

We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells.

cheers
shalin


Roger Tsien used to recommend putting diatom frustules into immersion oil with dye in it.

Jim P.


On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote:
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Why not use the everpresent molecular probes test slides?  FluoCells prepared slide #3 would be a likely candidate.  I use it for fluorescent and DIC alignment checks often.  It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs.  Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too.
--
Samuel A. Connell
Director of Light Microscopy
Cell & Tissue Imaging Center
St. Jude Children's Research Hospital
332 North Lauderdale St., E7061
Memphis, TN 38105-2794
(901) 495-2536
[hidden email]


________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Shalin Mehta [[hidden email]]
Sent: Thursday, June 19, 2008 7:47 PM
To: [hidden email]
Subject: Re: Source of Richardson test slide.    .

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara,
 EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email.
Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells.
btw folks, pardon the 'blurred' English in last mail.

cheers
Shalin


-- 
                   ****************************************
Prof. James B. Pawley,                                     Phone: 604-822-7801 
3D Microscopy of Living Cells: Summer Course   CELL: 778-861-2874    

"If it isn't diffraction, it is statistics":Microscopist's complaint, Anon.                 
Eric Scarfone Eric Scarfone
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Assymetric Illumination (Re: Source of Richardson test slide. .)

In reply to this post by Shalin Mehta
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello
Reading Shalin Mehta abstract I am not sure I understand how
assymetric illumination is achieved? I this is equivalent to the
technique used in video microscopy (ie: Kachar B. Asymmetric
illumination contrast: a method of image formation for video light
microscopy. Science. 1985 Feb 15;227(4688):766-8) shouldn't you put
half aperture stops at the back focal plane of the obejective and not
of the condenser? Or did I get it wrong?
Eric

 

Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work:  +46 (0)8-517 79343,
Cell:  +46 (0)70 888 2352
Fax:   +46 (0)8-301876

email:  [hidden email]
http://www.ki.se/cfh/


----- Original Message -----
From: Shalin Mehta <[hidden email]>
Date: Saturday, June 21, 2008 4:25 am
Subject: Re: Source of Richardson test slide. .
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I should have clarified. I am working on a method for imaging cell
> cultureson plastic in bas-relief. At the risk of self-promotion, I
> am posting link
> to the recent conference presentation:
> http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf
>
> We think it will be useful for quantitative (or atleast semi-
> quantitative)measurements of optical thickness. So I am looking
> for some well
> characterized test specimen (whose hight profile is known) which
> resembleoptical thickness of cells.
>
> cheers
> shalin
>
>
>
> On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel
> <[hidden email]>wrote:
>
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> >
> > Why not use the everpresent molecular probes test slides?  
FluoCells

> > prepared slide #3 would be a likely candidate.  I use it for
> fluorescent and
> > DIC alignment checks often.  It's 16um thick, so perhaps for an
> unknown> reason to me, that might not meet your needs.  Some of
> the other FluoCells
> > prepared slides are cultured cells rather than sections, so you
> might like
> > them too.
> > --
> > Samuel A. Connell
> > Director of Light Microscopy
> > Cell & Tissue Imaging Center
> > St. Jude Children's Research Hospital
> > 332 North Lauderdale St., E7061
> > Memphis, TN 38105-2794
> > (901) 495-2536
> > [hidden email]
> >
> >
> > ________________________________________
> > From: Confocal Microscopy List [[hidden email]]
> On Behalf
> > Of Shalin Mehta [[hidden email]]
> > Sent: Thursday, June 19, 2008 7:47 PM
> > To: [hidden email]
> > Subject: Re: Source of Richardson test slide.    .
> >
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks
> Barbara,>  EMS doesn't list the Richardson slide on website any
> more. I am waiting
> > for the reply to email.
> > Is there any other known phase contrast test specimen? One could
use
> > diatoms but they are rather 'active' optically. I would like
> something that
> > resembles (within a factor of 2 or 3) optical thickness of cells.
> > btw folks, pardon the 'blurred' English in last mail.
> >
> > cheers
> > Shalin
> >
>
Shalin Mehta Shalin Mehta
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Re: Assymetric Illumination (Re: Source of Richardson test slide. .)

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

You are almost correct.

Yes it is equivalent to Kachar's asymmetric illumination. Only reason Kachar is not mentioned in the abstract is lack of space, in my actual presentation I had motivated the phase gradient contrast without use of interference (as in DIC) from his paper.

Kachar had also used asymmetric illumination on condenser side. If you look at his Figure 2, he has offset the filament such that only one half of the condenser fills the BFP of condenser. Quating verbatim from his paper:

"To  obtain  asymmetric  illumination, 
the  lamp  filament  is  simply  displaced 
from the optical axis (Fig. 2a). With the 
filament offset, the regular diffuser glass 
in front of  the lamp spreads the light to 
fill the condenser aperture with a gradi- 
ent of  illumination (Fig. 2b). This gradi- 
ent provides the  requisite  imbalance of 
oblique rays. "

But you are right that putting a block in objective BFP will also produce phase gradient contrast (as is done by some researchers early and recently:
Axelrod - "Zero cost modification for phase imaging" or similar title
Jerome Mertz group - "Graded field microscopy white light microscopy" )

Of course, the problem with objective side block is that you lose NA. However, if that is the only thing accessible and one wants just phase gradient contrast, it is perfectly OK.

The difference is AI-DPC (as we like to call our method) is more quantitative in nature and separates phase information (optical thickness) and amplitude information (light absorbption) that you can super-impose later if you like.

We are in process of writing up the thing and if you like further details about quantitative nature we could discuss off-list.
We will also be very glad to see if some of you try this and have good/bad things to say about it.

Cheers
shalin





On Sat, Jun 21, 2008 at 11:26 PM, Eric Scarfone <[hidden email]> wrote:
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello
Reading Shalin Mehta abstract I am not sure I understand how
assymetric illumination is achieved? I this is equivalent to the
technique used in video microscopy (ie: Kachar B. Asymmetric
illumination contrast: a method of image formation for video light
microscopy. Science. 1985 Feb 15;227(4688):766-8) shouldn't you put
half aperture stops at the back focal plane of the obejective and not
of the condenser? Or did I get it wrong?
Eric



Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work:  +46 (0)8-517 79343,
Cell:  +46 (0)70 888 2352
Fax:   +46 (0)8-301876

email:  [hidden email]
http://www.ki.se/cfh/


----- Original Message -----
From: Shalin Mehta <[hidden email]>
Date: Saturday, June 21, 2008 4:25 am
Subject: Re: Source of Richardson test slide. .
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I should have clarified. I am working on a method for imaging cell
> cultureson plastic in bas-relief. At the risk of self-promotion, I
> am posting link
> to the recent conference presentation:
> http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf
>
> We think it will be useful for quantitative (or atleast semi-
> quantitative)measurements of optical thickness. So I am looking
> for some well
> characterized test specimen (whose hight profile is known) which
> resembleoptical thickness of cells.
>
> cheers
> shalin
>
>
>
> On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel
> <[hidden email]>wrote:
>
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> >
> > Why not use the everpresent molecular probes test slides?
FluoCells
> > prepared slide #3 would be a likely candidate.  I use it for
> fluorescent and
> > DIC alignment checks often.  It's 16um thick, so perhaps for an
> unknown> reason to me, that might not meet your needs.  Some of
> the other FluoCells
> > prepared slides are cultured cells rather than sections, so you
> might like
> > them too.
> > --
> > Samuel A. Connell
> > Director of Light Microscopy
> > Cell & Tissue Imaging Center
> > St. Jude Children's Research Hospital
> > 332 North Lauderdale St., E7061
> > Memphis, TN 38105-2794
> > (901) 495-2536
> > [hidden email]
> >
> >
> > ________________________________________
> > From: Confocal Microscopy List [[hidden email]]
> On Behalf
> > Of Shalin Mehta [[hidden email]]
> > Sent: Thursday, June 19, 2008 7:47 PM
> > To: [hidden email]
> > Subject: Re: Source of Richardson test slide.    .
> >
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks
> Barbara,>  EMS doesn't list the Richardson slide on website any
> more. I am waiting
> > for the reply to email.
> > Is there any other known phase contrast test specimen? One could
use
> > diatoms but they are rather 'active' optically. I would like
> something that
> > resembles (within a factor of 2 or 3) optical thickness of cells.
> > btw folks, pardon the 'blurred' English in last mail.
> >
> > cheers
> > Shalin
> >
>



--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm
Shalin Mehta Shalin Mehta
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Re: Source of Richardson test slide. .

In reply to this post by Shalin Mehta
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello Jim,

 Perhaps I didn't get it right - do you mean to say that a dye would deposit on frustule surface and I could get a 'reference' height profile from fluorescence stack? What dye should I use?

Cheers
Shalin

On Sat, Jun 21, 2008 at 12:14 PM, James Pawley <[hidden email]> wrote:
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have clarified. I am working on a method for imaging cell cultures on plastic in bas-relief. At the risk of self-promotion, I am posting link to the recent conference presentation: http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf


We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells.

cheers
shalin


Roger Tsien used to recommend putting diatom frustules into immersion oil with dye in it.

Jim P.


On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote:
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Why not use the everpresent molecular probes test slides?  FluoCells prepared slide #3 would be a likely candidate.  I use it for fluorescent and DIC alignment checks often.  It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs.  Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too.
--
Samuel A. Connell
Director of Light Microscopy
Cell & Tissue Imaging Center
St. Jude Children's Research Hospital
332 North Lauderdale St., E7061
Memphis, TN 38105-2794
(901) 495-2536
[hidden email]


________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Shalin Mehta [[hidden email]]
Sent: Thursday, June 19, 2008 7:47 PM
To: [hidden email]
Subject: Re: Source of Richardson test slide.    .

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara,
 EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email.
Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells.
btw folks, pardon the 'blurred' English in last mail.

cheers
Shalin


-- 
                   ****************************************
Prof. James B. Pawley,                                     Phone: 604-822-7801 
3D Microscopy of Living Cells: Summer Course   CELL: 778-861-2874    

"If it isn't diffraction, it is statistics":Microscopist's complaint, Anon.                 



--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm
Guy Cox Guy Cox
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Re: Source of Richardson test slide. .

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
I think the idea is that the dye will be a 'negative stain'.  But I have to
say that I don't think diatoms will be useful for your purpose since
the phase differences in the thicker areas such as the raphe are too
great and the structure in the thinner parts is too complex.  
 
Maybe one of the filter companies, who have the facilities for precise
deposition of layers of known refractive index, could create a 
patterned slide?  Any comments from the companies?
 
                                                                            Guy 
 

Optical Imaging Techniques in Cell Biology
by Guy Cox    CRC Press / Taylor & Francis
    http://www.guycox.com/optical.htm
______________________________________________
Associate Professor Guy Cox, MA, DPhil(Oxon)
Electron Microscope Unit, Madsen Building F09,
University of Sydney, NSW 2006
______________________________________________
Phone +61 2 9351 3176     Fax +61 2 9351 7682
Mobile 0413 281 861
______________________________________________
     http://www.guycox.net

 


From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Shalin Mehta
Sent: Sunday, 22 June 2008 1:26 PM
To: [hidden email]
Subject: Re: Source of Richardson test slide. .

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

 Perhaps I didn't get it right - do you mean to say that a dye would deposit on frustule surface and I could get a 'reference' height profile from fluorescence stack? What dye should I use?

Cheers
Shalin

On Sat, Jun 21, 2008 at 12:14 PM, James Pawley <[hidden email]> wrote:
Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have clarified. I am working on a method for imaging cell cultures on plastic in bas-relief. At the risk of self-promotion, I am posting link to the recent conference presentation: http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf


We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells.

cheers
shalin


Roger Tsien used to recommend putting diatom frustules into immersion oil with dye in it.

Jim P.


On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote:
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Why not use the everpresent molecular probes test slides?  FluoCells prepared slide #3 would be a likely candidate.  I use it for fluorescent and DIC alignment checks often.  It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs.  Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too.
--
Samuel A. Connell
Director of Light Microscopy
Cell & Tissue Imaging Center
St. Jude Children's Research Hospital
332 North Lauderdale St., E7061
Memphis, TN 38105-2794
(901) 495-2536
[hidden email]


________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Shalin Mehta [[hidden email]]
Sent: Thursday, June 19, 2008 7:47 PM
To: [hidden email]
Subject: Re: Source of Richardson test slide.    .

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara,
 EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email.
Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells.
btw folks, pardon the 'blurred' English in last mail.

cheers
Shalin


-- 
                   ****************************************
Prof. James B. Pawley,                                     Phone: 604-822-7801 
3D Microscopy of Living Cells: Summer Course   CELL: 778-861-2874    

"If it isn't diffraction, it is statistics":Microscopist's complaint, Anon.                 



--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm

No virus found in this incoming message.
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Shalin Mehta Shalin Mehta
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Re: Source of Richardson test slide. .

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

Thanks for clarification Guy.

'negative stain' is new to me. I agree with you about diatom's complex
structures - their periodic nature introduces diffraction effects of
their own and I have seen differences in contrast seen with cells and
diatoms. But in absence of other things, not bad to try. I found a
diatom on net that seems smooth - but no idea where to get it or
whether it has unresolved fine structure.

I will be glad to see if some company is willing to prepare a slide as
Guy suggests.

I have an inkling that AFM community has some transparent patterned
height standard to calibrate their equipment. I have seen a paper
(Spiral phase contrast imaging in microscopy) where measurements of
optical phase and AFM are compared. Still looking for it. Any word
from AFM people?

Is there an equivalent of confocal list for AFM that anyone knows of?
People around me who do AFM haven't yet suggested transparent test
slides.

Cheers
Shalin

On Sun, Jun 22, 2008 at 12:08 PM, Guy Cox <[hidden email]> wrote:

>
> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> I think the idea is that the dye will be a 'negative stain'.  But I have to
> say that I don't think diatoms will be useful for your purpose since
> the phase differences in the thicker areas such as the raphe are too
> great and the structure in the thinner parts is too complex.
>
> Maybe one of the filter companies, who have the facilities for precise
> deposition of layers of known refractive index, could create a
> patterned slide?  Any comments from the companies?
>
>                                                                             Guy
>
>
> Optical Imaging Techniques in Cell Biology
> by Guy Cox    CRC Press / Taylor & Francis
>     http://www.guycox.com/optical.htm
> ______________________________________________
> Associate Professor Guy Cox, MA, DPhil(Oxon)
> Electron Microscope Unit, Madsen Building F09,
> University of Sydney, NSW 2006
> ______________________________________________
> Phone +61 2 9351 3176     Fax +61 2 9351 7682
> Mobile 0413 281 861
> ______________________________________________
>      http://www.guycox.net
>
>
> ________________________________
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Shalin Mehta
> Sent: Sunday, 22 June 2008 1:26 PM
> To: [hidden email]
> Subject: Re: Source of Richardson test slide. .
>
> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello Jim,
>
>  Perhaps I didn't get it right - do you mean to say that a dye would deposit on frustule surface and I could get a 'reference' height profile from fluorescence stack? What dye should I use?
>
> Cheers
> Shalin
>
> On Sat, Jun 21, 2008 at 12:14 PM, James Pawley <[hidden email]> wrote:
>>
>> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have clarified. I am working on a method for imaging cell cultures on plastic in bas-relief. At the risk of self-promotion, I am posting link to the recent conference presentation: http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf
>>
>> We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells.
>>
>> cheers
>> shalin
>>
>>
>> Roger Tsien used to recommend putting diatom frustules into immersion oil with dye in it.
>> Jim P.
>>
>> On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote:
>>
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> Why not use the everpresent molecular probes test slides?  FluoCells prepared slide #3 would be a likely candidate.  I use it for fluorescent and DIC alignment checks often.  It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs.  Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too.
>> --
>> Samuel A. Connell
>> Director of Light Microscopy
>> Cell & Tissue Imaging Center
>> St. Jude Children's Research Hospital
>> 332 North Lauderdale St., E7061
>> Memphis, TN 38105-2794
>> (901) 495-2536
>> [hidden email]
>>
>>
>> ________________________________________
>> From: Confocal Microscopy List [[hidden email]] On Behalf Of Shalin Mehta [[hidden email]]
>> Sent: Thursday, June 19, 2008 7:47 PM
>> To: [hidden email]
>> Subject: Re: Source of Richardson test slide.    .
>>
>> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara,
>>  EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email.
>> Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells.
>> btw folks, pardon the 'blurred' English in last mail.
>>
>> cheers
>> Shalin
>>
>> --
>>
>>                    ****************************************
>> Prof. James B. Pawley,                                     Phone: 604-822-7801
>> 3D Microscopy of Living Cells: Summer Course   CELL: 778-861-2874
>>
>> "If it isn't diffraction, it is statistics":Microscopist's complaint, Anon.
>
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~
> Shalin Mehta
> mobile: +65-90694182
> blog: shalin.wordpress.com
> ~~~~~~~~~~~~~~~~~~~~~~~~~~
> Bioimaging Lab, Block-E3A, #7-10
> Div of Bioengineering, NUS Singapore 117574
> website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html
>
> Liver Cancer Functional Genomics Lab, #6-05
> National Cancer Centre, Singapore 169610
> http://www.nccs.com.sg/researcher/02_04d.htm
>
> No virus found in this incoming message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM
>
> No virus found in this outgoing message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM



--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm
Guy Cox Guy Cox
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Open this post in threaded view
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Re: Source of Richardson test slide. .

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

Negative staining simply means surrounding an unstained sample
with a sea of stain.  In principle this will just give a negative
image compared to conventional staining.

I used to have a glass slide with a known step in it but it
was supplied as a calibration standard with a 'tally-step'
(DekTak I think) so I don't know where you could buy one.
That one got broken.  But it would probably be worth checking
the Agar Scientific catalogue - they're pretty good for such
things.  

                                           Guy



Optical Imaging Techniques in Cell Biology
by Guy Cox    CRC Press / Taylor & Francis
    http://www.guycox.com/optical.htm
______________________________________________
Associate Professor Guy Cox, MA, DPhil(Oxon)
Electron Microscope Unit, Madsen Building F09,
University of Sydney, NSW 2006
______________________________________________
Phone +61 2 9351 3176     Fax +61 2 9351 7682
Mobile 0413 281 861
______________________________________________
     http://www.guycox.net
-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Shalin Mehta
Sent: Sunday, 22 June 2008 2:34 PM
To: [hidden email]
Subject: Re: Source of Richardson test slide. .

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

Thanks for clarification Guy.

'negative stain' is new to me. I agree with you about diatom's complex structures - their periodic nature introduces diffraction effects of their own and I have seen differences in contrast seen with cells and diatoms. But in absence of other things, not bad to try. I found a diatom on net that seems smooth - but no idea where to get it or whether it has unresolved fine structure.

I will be glad to see if some company is willing to prepare a slide as Guy suggests.

I have an inkling that AFM community has some transparent patterned height standard to calibrate their equipment. I have seen a paper (Spiral phase contrast imaging in microscopy) where measurements of optical phase and AFM are compared. Still looking for it. Any word from AFM people?

Is there an equivalent of confocal list for AFM that anyone knows of?
People around me who do AFM haven't yet suggested transparent test slides.

Cheers
Shalin

On Sun, Jun 22, 2008 at 12:08 PM, Guy Cox <[hidden email]> wrote:

>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> I think the idea is that the dye will be a 'negative stain'.  But I
> have to say that I don't think diatoms will be useful for your purpose
> since the phase differences in the thicker areas such as the raphe are
> too great and the structure in the thinner parts is too complex.
>
> Maybe one of the filter companies, who have the facilities for precise
> deposition of layers of known refractive index, could create a
> patterned slide?  Any comments from the companies?
>
>                                                                            
> Guy
>
>
> Optical Imaging Techniques in Cell Biology
> by Guy Cox    CRC Press / Taylor & Francis
>     http://www.guycox.com/optical.htm
> ______________________________________________
> Associate Professor Guy Cox, MA, DPhil(Oxon) Electron Microscope Unit,
> Madsen Building F09, University of Sydney, NSW 2006
> ______________________________________________
> Phone +61 2 9351 3176     Fax +61 2 9351 7682
> Mobile 0413 281 861
> ______________________________________________
>      http://www.guycox.net
>
>
> ________________________________
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Shalin Mehta
> Sent: Sunday, 22 June 2008 1:26 PM
> To: [hidden email]
> Subject: Re: Source of Richardson test slide. .
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello Jim,
>
>  Perhaps I didn't get it right - do you mean to say that a dye would deposit on frustule surface and I could get a 'reference' height profile from fluorescence stack? What dye should I use?
>
> Cheers
> Shalin
>
> On Sat, Jun 21, 2008 at 12:14 PM, James Pawley <[hidden email]> wrote:
>>
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I should have
>> clarified. I am working on a method for imaging cell cultures on
>> plastic in bas-relief. At the risk of self-promotion, I am posting
>> link to the recent conference presentation:
>> http://www.focusonmicroscopy.org/2008/PDF/089_Mehta.pdf
>>
>> We think it will be useful for quantitative (or atleast semi-quantitative) measurements of optical thickness. So I am looking for some well characterized test specimen (whose hight profile is known) which resemble optical thickness of cells.
>>
>> cheers
>> shalin
>>
>>
>> Roger Tsien used to recommend putting diatom frustules into immersion oil with dye in it.
>> Jim P.
>>
>> On Fri, Jun 20, 2008 at 8:19 PM, Connell, Samuel <[hidden email]> wrote:
>>
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> Why not use the everpresent molecular probes test slides?  FluoCells prepared slide #3 would be a likely candidate.  I use it for fluorescent and DIC alignment checks often.  It's 16um thick, so perhaps for an unknown reason to me, that might not meet your needs.  Some of the other FluoCells prepared slides are cultured cells rather than sections, so you might like them too.
>> --
>> Samuel A. Connell
>> Director of Light Microscopy
>> Cell & Tissue Imaging Center
>> St. Jude Children's Research Hospital
>> 332 North Lauderdale St., E7061
>> Memphis, TN 38105-2794
>> (901) 495-2536
>> [hidden email]
>>
>>
>> ________________________________________
>> From: Confocal Microscopy List [[hidden email]] On
>> Behalf Of Shalin Mehta [[hidden email]]
>> Sent: Thursday, June 19, 2008 7:47 PM
>> To: [hidden email]
>> Subject: Re: Source of Richardson test slide.    .
>>
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Thanks Barbara,  EMS doesn't list the Richardson slide on website any more. I am waiting for the reply to email.
>> Is there any other known phase contrast test specimen? One could use diatoms but they are rather 'active' optically. I would like something that resembles (within a factor of 2 or 3) optical thickness of cells.
>> btw folks, pardon the 'blurred' English in last mail.
>>
>> cheers
>> Shalin
>>
>> --
>>
>>                    ****************************************
>> Prof. James B. Pawley,                                     Phone: 604-822-7801
>> 3D Microscopy of Living Cells: Summer Course   CELL: 778-861-2874
>>
>> "If it isn't diffraction, it is statistics":Microscopist's complaint, Anon.
>
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~
> Shalin Mehta
> mobile: +65-90694182
> blog: shalin.wordpress.com
> ~~~~~~~~~~~~~~~~~~~~~~~~~~
> Bioimaging Lab, Block-E3A, #7-10
> Div of Bioengineering, NUS Singapore 117574
> website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html
>
> Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre,
> Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm
>
> No virus found in this incoming message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date:
> 21/06/2008 9:27 AM
>
> No virus found in this outgoing message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date:
> 21/06/2008 9:27 AM



--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05 National Cancer Centre, Singapore 169610 http://www.nccs.com.sg/researcher/02_04d.htm

No virus found in this incoming message.
Checked by AVG.
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John Oreopoulos John Oreopoulos
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An alarming amount of image manipulation

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

I was a bit surprised at the statistics cited in this article:

http://chronicle.com/free/2008/05/3028n.htm

Does this mean that all journals will start hiring image manipulation  
detectives someday? Could be an interesting career.


John Oreopoulos, BSc,
PhD Candidate
University of Toronto
Institute For Biomaterials and Biomedical Engineering
Centre For Studies in Molecular Imaging

Tel: W:416-946-5022
Guy Cox Guy Cox
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Re: An alarming amount of image manipulation

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

Interesting - especially the statement that images on film
cannot be doctored. I guess it's irrelevant nowadays, but that
is so far from the truth.

One funny story - which I've told before but some time ago.
Many years ago I (with colleagues) published a paper in a
well-known journal which included a photo of some gels -
taken by the departmental photographer.  One of the gels had
cracked when it was taken out of the tube, so there was a
dark hairline across it in the photo.  In the published paper
that line had disappeared.  You can hardly accuse me, or my
two co-authors, of fraud since this was done by the journal's
art department without any reference to us!

                                                       Guy


Optical Imaging Techniques in Cell Biology
by Guy Cox    CRC Press / Taylor & Francis
    http://www.guycox.com/optical.htm
______________________________________________
Associate Professor Guy Cox, MA, DPhil(Oxon)
Electron Microscope Unit, Madsen Building F09,
University of Sydney, NSW 2006
______________________________________________
Phone +61 2 9351 3176     Fax +61 2 9351 7682
Mobile 0413 281 861
______________________________________________
     http://www.guycox.net
-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos
Sent: Sunday, 22 June 2008 10:57 PM
To: [hidden email]
Subject: An alarming amount of image manipulation

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

I was a bit surprised at the statistics cited in this article:

http://chronicle.com/free/2008/05/3028n.htm

Does this mean that all journals will start hiring image manipulation detectives someday? Could be an interesting career.


John Oreopoulos, BSc,
PhD Candidate
University of Toronto
Institute For Biomaterials and Biomedical Engineering Centre For Studies in Molecular Imaging

Tel: W:416-946-5022

No virus found in this incoming message.
Checked by AVG.
Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM
 

No virus found in this outgoing message.
Checked by AVG.
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Shalin Mehta Shalin Mehta
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Re: An alarming amount of image manipulation

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

We realized it is a big concern these days when we took a course on
ethics in research (mandatory for anyone doing bioengineering or life
sciences here). We came across quite interesting cases of high profile
fraud.

We had to do a presentation and we presented something on image
manipulation. While thinking about it I stumbled upon an interesting
way of quickly checking fake data. It is to 'scan the histogram' with
'narrow look up table', i.e. set the contrast to maximum and view the
image as you change the brightness.

The idea being that when someone has merged different images to appear
one or copied e.g. bands - scanning the histogram will show clear
signs. In the case of merging,one can see an edge where merge has been
done and in the case of copy one can see that two regions of the image
change identically as we scan the histogram. With that, I found that I
could actually detect discrepancies in example fake data given in
Rossner's editorial (What is in a picture? by Rossner and Yamada).

I tend to think that these problems will subside as ideas like open
source, reproducible research
(http://sepwww.stanford.edu/research/redoc/), and giving credit based
on 'first appearance anywhere and not just journal' will permeate
gradually - they have already done so in computer science where it is
very easy to allow someone to reproduce your work simply by uploading
files.

cheers
shalin



On Sun, Jun 22, 2008 at 10:43 PM, Guy Cox <[hidden email]> wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Interesting - especially the statement that images on film
> cannot be doctored. I guess it's irrelevant nowadays, but that
> is so far from the truth.
>
> One funny story - which I've told before but some time ago.
> Many years ago I (with colleagues) published a paper in a
> well-known journal which included a photo of some gels -
> taken by the departmental photographer.  One of the gels had
> cracked when it was taken out of the tube, so there was a
> dark hairline across it in the photo.  In the published paper
> that line had disappeared.  You can hardly accuse me, or my
> two co-authors, of fraud since this was done by the journal's
> art department without any reference to us!
>
>                                                       Guy
>
>
> Optical Imaging Techniques in Cell Biology
> by Guy Cox    CRC Press / Taylor & Francis
>    http://www.guycox.com/optical.htm
> ______________________________________________
> Associate Professor Guy Cox, MA, DPhil(Oxon)
> Electron Microscope Unit, Madsen Building F09,
> University of Sydney, NSW 2006
> ______________________________________________
> Phone +61 2 9351 3176     Fax +61 2 9351 7682
> Mobile 0413 281 861
> ______________________________________________
>     http://www.guycox.net
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos
> Sent: Sunday, 22 June 2008 10:57 PM
> To: [hidden email]
> Subject: An alarming amount of image manipulation
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I was a bit surprised at the statistics cited in this article:
>
> http://chronicle.com/free/2008/05/3028n.htm
>
> Does this mean that all journals will start hiring image manipulation detectives someday? Could be an interesting career.
>
>
> John Oreopoulos, BSc,
> PhD Candidate
> University of Toronto
> Institute For Biomaterials and Biomedical Engineering Centre For Studies in Molecular Imaging
>
> Tel: W:416-946-5022
>
> No virus found in this incoming message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM
>
>
> No virus found in this outgoing message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008 9:27 AM
>
>



--
~~~~~~~~~~~~~~~~~~~~~~~~~
Shalin Mehta
mobile: +65-90694182
blog: shalin.wordpress.com
~~~~~~~~~~~~~~~~~~~~~~~~~~
Bioimaging Lab, Block-E3A, #7-10
Div of Bioengineering, NUS Singapore 117574
website: http://www.bioeng.nus.edu.sg/optbioimaging/colin/index.html

Liver Cancer Functional Genomics Lab, #6-05
National Cancer Centre, Singapore 169610
http://www.nccs.com.sg/researcher/02_04d.htm
Michael Cammer Michael Cammer
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Re: An alarming amount of image manipulation

In reply to this post by Guy Cox
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

In my experience, when somebody shows up with micrographs that have cells
pasted in or background "distractions" stamp tooled out and I suggest
maybe taking more pictures or doing the experiment again, they complain
that this would cost more and delay them.  "The data are what they are and
I'm just showing people and if I don't make it look good, then they won't
publish it."  Sometimes junior lab members will go back to their PIs and
say that I wasn't helpful; I become the problem.  I will not apologize for
refusing to use the lasso tool around a band on a gel and S curve adjust
it in Photoshop Curves or for refusing to paint out "an anomalous bad cell
off in the corner of the image".  Yes, both these requests have come
through our facility along with a bunch of other egregious ones.  Some
scientists really feel justified because the competition does it.  "Hey,
everybody does it," they say.  Although, more often (and a search will
show that we've discussed this before), people simply don;t understand
what they are doing.  They simply misuse the tools for making figures.  As
with example of film, before you can begin to alter images in an
intentional manner or make even reasonably good pictures of anything, you
need to be at least knowledgeable of darkroom technique.  But with the new
digital tools, any dummy can be a photographer and can cut and paste and
manipulate in complicated ways.
-Michael

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Interesting - especially the statement that images on film
> cannot be doctored. I guess it's irrelevant nowadays, but that
> is so far from the truth.
>
> One funny story - which I've told before but some time ago.
> Many years ago I (with colleagues) published a paper in a
> well-known journal which included a photo of some gels -
> taken by the departmental photographer.  One of the gels had
> cracked when it was taken out of the tube, so there was a
> dark hairline across it in the photo.  In the published paper
> that line had disappeared.  You can hardly accuse me, or my
> two co-authors, of fraud since this was done by the journal's
> art department without any reference to us!
>
>                                                        Guy
>
>
> Optical Imaging Techniques in Cell Biology
> by Guy Cox    CRC Press / Taylor & Francis
>     http://www.guycox.com/optical.htm
> ______________________________________________
> Associate Professor Guy Cox, MA, DPhil(Oxon)
> Electron Microscope Unit, Madsen Building F09,
> University of Sydney, NSW 2006
> ______________________________________________
> Phone +61 2 9351 3176     Fax +61 2 9351 7682
> Mobile 0413 281 861
> ______________________________________________
>      http://www.guycox.net
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On
> Behalf Of John Oreopoulos
> Sent: Sunday, 22 June 2008 10:57 PM
> To: [hidden email]
> Subject: An alarming amount of image manipulation
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I was a bit surprised at the statistics cited in this article:
>
> http://chronicle.com/free/2008/05/3028n.htm
>
> Does this mean that all journals will start hiring image manipulation
> detectives someday? Could be an interesting career.
>
>
> John Oreopoulos, BSc,
> PhD Candidate
> University of Toronto
> Institute For Biomaterials and Biomedical Engineering Centre For Studies
> in Molecular Imaging
>
> Tel: W:416-946-5022
>
> No virus found in this incoming message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008
> 9:27 AM
>
>
> No virus found in this outgoing message.
> Checked by AVG.
> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008
> 9:27 AM
>
>


_________________________________________
Michael Cammer   http://www.aecom.yu.edu/aif/
dc-4 dc-4
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Re: An alarming amount of image manipulation

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

Oh for the days of dye-sublimation printers and the tell-tale snail trails
of poorly executed "touch-up" jobs.

DC

--------------------------------------------------
From: "Michael Cammer" <[hidden email]>
Sent: Sunday, June 22, 2008 5:30 PM
To: <[hidden email]>
Subject: Re: An alarming amount of image manipulation

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> In my experience, when somebody shows up with micrographs that have cells
> pasted in or background "distractions" stamp tooled out and I suggest
> maybe taking more pictures or doing the experiment again, they complain
> that this would cost more and delay them.  "The data are what they are and
> I'm just showing people and if I don't make it look good, then they won't
> publish it."  Sometimes junior lab members will go back to their PIs and
> say that I wasn't helpful; I become the problem.  I will not apologize for
> refusing to use the lasso tool around a band on a gel and S curve adjust
> it in Photoshop Curves or for refusing to paint out "an anomalous bad cell
> off in the corner of the image".  Yes, both these requests have come
> through our facility along with a bunch of other egregious ones.  Some
> scientists really feel justified because the competition does it.  "Hey,
> everybody does it," they say.  Although, more often (and a search will
> show that we've discussed this before), people simply don;t understand
> what they are doing.  They simply misuse the tools for making figures.  As
> with example of film, before you can begin to alter images in an
> intentional manner or make even reasonably good pictures of anything, you
> need to be at least knowledgeable of darkroom technique.  But with the new
> digital tools, any dummy can be a photographer and can cut and paste and
> manipulate in complicated ways.
> -Michael
>
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> Interesting - especially the statement that images on film
>> cannot be doctored. I guess it's irrelevant nowadays, but that
>> is so far from the truth.
>>
>> One funny story - which I've told before but some time ago.
>> Many years ago I (with colleagues) published a paper in a
>> well-known journal which included a photo of some gels -
>> taken by the departmental photographer.  One of the gels had
>> cracked when it was taken out of the tube, so there was a
>> dark hairline across it in the photo.  In the published paper
>> that line had disappeared.  You can hardly accuse me, or my
>> two co-authors, of fraud since this was done by the journal's
>> art department without any reference to us!
>>
>>                                                        Guy
>>
>>
>> Optical Imaging Techniques in Cell Biology
>> by Guy Cox    CRC Press / Taylor & Francis
>>     http://www.guycox.com/optical.htm
>> ______________________________________________
>> Associate Professor Guy Cox, MA, DPhil(Oxon)
>> Electron Microscope Unit, Madsen Building F09,
>> University of Sydney, NSW 2006
>> ______________________________________________
>> Phone +61 2 9351 3176     Fax +61 2 9351 7682
>> Mobile 0413 281 861
>> ______________________________________________
>>      http://www.guycox.net
>> -----Original Message-----
>> From: Confocal Microscopy List [mailto:[hidden email]] On
>> Behalf Of John Oreopoulos
>> Sent: Sunday, 22 June 2008 10:57 PM
>> To: [hidden email]
>> Subject: An alarming amount of image manipulation
>>
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> I was a bit surprised at the statistics cited in this article:
>>
>> http://chronicle.com/free/2008/05/3028n.htm
>>
>> Does this mean that all journals will start hiring image manipulation
>> detectives someday? Could be an interesting career.
>>
>>
>> John Oreopoulos, BSc,
>> PhD Candidate
>> University of Toronto
>> Institute For Biomaterials and Biomedical Engineering Centre For Studies
>> in Molecular Imaging
>>
>> Tel: W:416-946-5022
>>
>> No virus found in this incoming message.
>> Checked by AVG.
>> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date:
>> 21/06/2008
>> 9:27 AM
>>
>>
>> No virus found in this outgoing message.
>> Checked by AVG.
>> Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date:
>> 21/06/2008
>> 9:27 AM
>>
>>
>
>
> _________________________________________
> Michael Cammer   http://www.aecom.yu.edu/aif/
>
>
David Barnes-2 David Barnes-2
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Re: An alarming amount of image manipulation

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Good reason why the forensic community is "leary" of Photoshop.
 
My former company "invented" the tracking process of processes applied circa 1990.
 
"latentpro" was the most widely used IP package for many years...

On Sun, Jun 22, 2008 at 4:15 PM, Darran Clements <[hidden email]> wrote:
Oh for the days of dye-sublimation printers and the tell-tale snail trails of poorly executed "touch-up" jobs.

DC

--------------------------------------------------
From: "Michael Cammer" <[hidden email]>
Sent: Sunday, June 22, 2008 5:30 PM Subject: Re: An alarming amount of image manipulation


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

In my experience, when somebody shows up with micrographs that have cells
pasted in or background "distractions" stamp tooled out and I suggest
maybe taking more pictures or doing the experiment again, they complain
that this would cost more and delay them.  "The data are what they are and
I'm just showing people and if I don't make it look good, then they won't
publish it."  Sometimes junior lab members will go back to their PIs and
say that I wasn't helpful; I become the problem.  I will not apologize for
refusing to use the lasso tool around a band on a gel and S curve adjust
it in Photoshop Curves or for refusing to paint out "an anomalous bad cell
off in the corner of the image".  Yes, both these requests have come
through our facility along with a bunch of other egregious ones.  Some
scientists really feel justified because the competition does it.  "Hey,
everybody does it," they say.  Although, more often (and a search will
show that we've discussed this before), people simply don;t understand
what they are doing.  They simply misuse the tools for making figures.  As
with example of film, before you can begin to alter images in an
intentional manner or make even reasonably good pictures of anything, you
need to be at least knowledgeable of darkroom technique.  But with the new
digital tools, any dummy can be a photographer and can cut and paste and
manipulate in complicated ways.
-Michael

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

Interesting - especially the statement that images on film
cannot be doctored. I guess it's irrelevant nowadays, but that
is so far from the truth.

One funny story - which I've told before but some time ago.
Many years ago I (with colleagues) published a paper in a
well-known journal which included a photo of some gels -
taken by the departmental photographer.  One of the gels had
cracked when it was taken out of the tube, so there was a
dark hairline across it in the photo.  In the published paper
that line had disappeared.  You can hardly accuse me, or my
two co-authors, of fraud since this was done by the journal's
art department without any reference to us!

                                                      Guy


Optical Imaging Techniques in Cell Biology
by Guy Cox    CRC Press / Taylor & Francis
   http://www.guycox.com/optical.htm
______________________________________________
Associate Professor Guy Cox, MA, DPhil(Oxon)
Electron Microscope Unit, Madsen Building F09,
University of Sydney, NSW 2006
______________________________________________
Phone +61 2 9351 3176     Fax +61 2 9351 7682
Mobile 0413 281 861
______________________________________________
    http://www.guycox.net
-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of John Oreopoulos
Sent: Sunday, 22 June 2008 10:57 PM
To: [hidden email]
Subject: An alarming amount of image manipulation

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

I was a bit surprised at the statistics cited in this article:

http://chronicle.com/free/2008/05/3028n.htm

Does this mean that all journals will start hiring image manipulation
detectives someday? Could be an interesting career.


John Oreopoulos, BSc,
PhD Candidate
University of Toronto
Institute For Biomaterials and Biomedical Engineering Centre For Studies
in Molecular Imaging

Tel: W:416-946-5022

No virus found in this incoming message.
Checked by AVG.
Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008
9:27 AM


No virus found in this outgoing message.
Checked by AVG.
Version: 7.5.524 / Virus Database: 270.4.1/1512 - Release Date: 21/06/2008
9:27 AM




_________________________________________
Michael Cammer   http://www.aecom.yu.edu/aif/



ian gibbins ian gibbins
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Re: An alarming amount of image manipulation

In reply to this post by John Oreopoulos
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

There is a good article on all this in the most recent edition of
Scientific American. It shows how digital image detectives can detect
some pretty subtle manipulations. They are mostly looking at press
images, but many of the principles apply to microscopy and other
lab-generated images. Well worth a read, even if it might take the
sparkle from your eye!

IAN


On Sunday, June 22, 2008, at 10:27  PM, John Oreopoulos wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I was a bit surprised at the statistics cited in this article:
>
> http://chronicle.com/free/2008/05/3028n.htm
>
> Does this mean that all journals will start hiring image manipulation
> detectives someday? Could be an interesting career.
>
>
> John Oreopoulos, BSc,
> PhD Candidate
> University of Toronto
> Institute For Biomaterials and Biomedical Engineering
> Centre For Studies in Molecular Imaging
>
> Tel: W:416-946-5022
>
>

* * * * * * * * * * *
Prof Ian Gibbins
Anatomy & Histology
Flinders University
GPO Box 2100
Adelaide SA 5001
AUSTRALIA

[hidden email]
voice: +61-8-8204 5271
fax: +61-8-8277 0085

http://som.flinders.edu.au/FUSA/Anatomy/
http://www.flinders.edu.au/neuroscience
Tina Carvalho Tina Carvalho
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Re: An alarming amount of image manipulation

In reply to this post by John Oreopoulos
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

So this might be a good time to remind everyone that the Microscopy
Society of America's Education Committee has a subcommittee on the Ethics
of Digital Imaging. Several years ago we tackled this problem
(intellectually) and came up with amazingly straightforward guidelines:

The only thing you can do to a digital image without reporting it as
manipulation is changing contrast and brightness, and levels/gamma/curves
over the entire image. *Anything* else needs to be reported as an image
manipulation in the Materials and Methods. In addition, the original
(unmanipulated) image must be stored as an uncompressed TIFF on archival
media. It should be available to anyone who requests inspecting the
original.

We hoped that this would alert (un-educated) researchers to the fact
that Photoshoping an image means changing the data, and they would
educate themselves about image manipulation programs and how they work and
what they are actually dong to an image.

Now, of course there are all kinds of things you can do before
snapping/saving an image, especially with confocal and fluorescence
acquisition software, and we have to rely on people's internal morality
meter... But even there researchers should be able to adequately report
and describe their software and parameters. If they can't, it's probably
more a matter of not understanding what they are doing, a problem that
seems to be rampant these days. Of course, there is also the question of
deliberate fraud, but I suspect that's truly less that is insinuated in
the article and more a question of un-education.

Aloha, Tina

> I was a bit surprised at the statistics cited in this article:
>
> http://chronicle.com/free/2008/05/3028n.htm
>
> Does this mean that all journals will start hiring image manipulation  
> detectives someday? Could be an interesting career.
>
>
> John Oreopoulos, BSc,
> PhD Candidate
> University of Toronto
> Institute For Biomaterials and Biomedical Engineering
> Centre For Studies in Molecular Imaging
>
> Tel: W:416-946-5022
>

****************************************************************************
* Tina (Weatherby) Carvalho               * [hidden email]           *
* Biological Electron Microscope Facility * (808) 956-6251                 *
* University of Hawaii at Manoa           * http://www.pbrc.hawaii.edu/bemf* 
****************************************************************************
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