advice wanted

[Maria Y. Boulina]

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Folks,

I need your advice on what to do with a manuscript. The story is, we have been working
on a quantification protocol for a while with a student on her large-scale imaging project.
We spent some brain power on it, so at the end, we have decided to publish it as a small
methods paper. the novelty of our approach was applying the Nyquist sampling rate to
the target object size, rather than the confocal system output AND adequate post-
processing. we have shown that 1)our suggested algorithm works well in terms of
preserving the number of counts acquired, compared to higher sampling rates; and allows
to  keep image size/sampling density/imaging time about several fold lower than you
would do standard 2)if you neglect proper sampling rates (linked to the object size!) or
skip processing, your results suck.

we have sent the paper to two journals, and received three sets of comments

reviewer 1: overall correct, but...nothing new .. AND(!!)... In many studies,
photobleaching is a major determinant of the spatial sampling rate to use

other journal

reviewer 2:
..a pipeline for speckle counting on the CellProfiler example page that seems relevant...
and..the use of passive voice throughout makes it a difficult and dry read..

reviewer 3:

The authors fail to demonstrate that using this method increases the accuracy of their
quantitation (We were aiming at preserving the accuracy and minimizing the effort!!).

This method is not broadly applicable (???, almost  every lab has to quantify images).  

My main idea behind submitting the manuscript was, that its always nice to have an
example of a working protocol, and sampling rate is something often neglected (see
comments from reviewer 1). I have seen tons of very smart grad students, who need to
do quantification, but end up performing manual counting on their images, since adapting
existing protocols is beyond their available effort. On the other hand, I am personally not
qualified to go deep into physics and math behind sampling according to the PSF of the
system vs sampling based on object density. However, I know that sampling below
Nyquist is hot in medical imaging field now.

I can not publish the full method within the main paper from the study. Quit? Try other
microscopy journals? Publish on the Core's webpage?

[Nuno Moreno]

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Dear Maria

Its is true that there is little room for methodologies developed in core facilities. They might be of great value for the community but scientifically not so relevant or new.

This was one of the reasons why we just release an award targeting exactly this kind of work. The award has international and independent reviewers. Therefore, on top of the prize (a macbook for you and our software for 2 years for your institution), there is also the international recognition.

More details at  
cirklo.org  (follow the prize link)

Good luck with your application!

All the best
Nuno Moreno

> On 20 May 2015, at 15:30, Maria Y. Boulina <[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Folks,
>
> I need your advice on what to do with a manuscript. The story is, we have been working
> on a quantification protocol for a while with a student on her large-scale imaging project.
> We spent some brain power on it, so at the end, we have decided to publish it as a small
> methods paper. the novelty of our approach was applying the Nyquist sampling rate to
> the target object size, rather than the confocal system output AND adequate post-
> processing. we have shown that 1)our suggested algorithm works well in terms of
> preserving the number of counts acquired, compared to higher sampling rates; and allows
> to  keep image size/sampling density/imaging time about several fold lower than you
> would do standard 2)if you neglect proper sampling rates (linked to the object size!) or
> skip processing, your results suck.
>
> we have sent the paper to two journals, and received three sets of comments
>
> reviewer 1: overall correct, but...nothing new .. AND(!!)... In many studies,
> photobleaching is a major determinant of the spatial sampling rate to use
>
> other journal
>
> reviewer 2:
> ..a pipeline for speckle counting on the CellProfiler example page that seems relevant...
> and..the use of passive voice throughout makes it a difficult and dry read..
>
> reviewer 3:
>
> The authors fail to demonstrate that using this method increases the accuracy of their
> quantitation (We were aiming at preserving the accuracy and minimizing the effort!!).
>
> This method is not broadly applicable (???, almost  every lab has to quantify images).  
>
> My main idea behind submitting the manuscript was, that its always nice to have an
> example of a working protocol, and sampling rate is something often neglected (see
> comments from reviewer 1). I have seen tons of very smart grad students, who need to
> do quantification, but end up performing manual counting on their images, since adapting
> existing protocols is beyond their available effort. On the other hand, I am personally not
> qualified to go deep into physics and math behind sampling according to the PSF of the
> system vs sampling based on object density. However, I know that sampling below
> Nyquist is hot in medical imaging field now.
>
> I can not publish the full method within the main paper from the study. Quit? Try other
> microscopy journals? Publish on the Core's webpage?

[Craig Brideau]

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*****

Have you considered an Engineering journal like SPIE Biophotonics? They
might be more appreciative of a sampling technique, and since they went
open access their impact factor has started to climb a bit. It was fairly
exclusive before going open.

Craig
On May 20, 2015 8:32 AM, "Maria Y. Boulina" <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Folks,
>
> I need your advice on what to do with a manuscript. The story is, we have
> been working
> on a quantification protocol for a while with a student on her large-scale
> imaging project.
> We spent some brain power on it, so at the end, we have decided to publish
> it as a small
> methods paper. the novelty of our approach was applying the Nyquist
> sampling rate to
> the target object size, rather than the confocal system output AND
> adequate post-
> processing. we have shown that 1)our suggested algorithm works well in
> terms of
> preserving the number of counts acquired, compared to higher sampling
> rates; and allows
> to  keep image size/sampling density/imaging time about several fold lower
> than you
> would do standard 2)if you neglect proper sampling rates (linked to the
> object size!) or
> skip processing, your results suck.
>
> we have sent the paper to two journals, and received three sets of comments
>
> reviewer 1: overall correct, but...nothing new .. AND(!!)... In many
> studies,
> photobleaching is a major determinant of the spatial sampling rate to use
>
> other journal
>
> reviewer 2:
> ..a pipeline for speckle counting on the CellProfiler example page that
> seems relevant...
> and..the use of passive voice throughout makes it a difficult and dry
> read..
>
> reviewer 3:
>
> The authors fail to demonstrate that using this method increases the
> accuracy of their
> quantitation (We were aiming at preserving the accuracy and minimizing the
> effort!!).
>
> This method is not broadly applicable (???, almost  every lab has to
> quantify images).
>
> My main idea behind submitting the manuscript was, that its always nice to
> have an
> example of a working protocol, and sampling rate is something often
> neglected (see
> comments from reviewer 1). I have seen tons of very smart grad students,
> who need to
> do quantification, but end up performing manual counting on their images,
> since adapting
> existing protocols is beyond their available effort. On the other hand, I
> am personally not
> qualified to go deep into physics and math behind sampling according to
> the PSF of the
> system vs sampling based on object density. However, I know that sampling
> below
> Nyquist is hot in medical imaging field now.
>
> I can not publish the full method within the main paper from the study.
> Quit? Try other
> microscopy journals? Publish on the Core's webpage?
>

[Kurt Thorn]

*****
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*****

I would also look at PLoS One - they are not supposed to evaluate on
impact, just on scientific correctness.  The one paper I published there
was a fairly easy process. It is open access with publishing charges.

Kurt

On 5/20/2015 8:22 AM, Craig Brideau wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Have you considered an Engineering journal like SPIE Biophotonics? They
> might be more appreciative of a sampling technique, and since they went
> open access their impact factor has started to climb a bit. It was fairly
> exclusive before going open.
>
> Craig
> On May 20, 2015 8:32 AM, "Maria Y. Boulina" <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Folks,
>>
>> I need your advice on what to do with a manuscript. The story is, we have
>> been working
>> on a quantification protocol for a while with a student on her large-scale
>> imaging project.
>> We spent some brain power on it, so at the end, we have decided to publish
>> it as a small
>> methods paper. the novelty of our approach was applying the Nyquist
>> sampling rate to
>> the target object size, rather than the confocal system output AND
>> adequate post-
>> processing. we have shown that 1)our suggested algorithm works well in
>> terms of
>> preserving the number of counts acquired, compared to higher sampling
>> rates; and allows
>> to  keep image size/sampling density/imaging time about several fold lower
>> than you
>> would do standard 2)if you neglect proper sampling rates (linked to the
>> object size!) or
>> skip processing, your results suck.
>>
>> we have sent the paper to two journals, and received three sets of comments
>>
>> reviewer 1: overall correct, but...nothing new .. AND(!!)... In many
>> studies,
>> photobleaching is a major determinant of the spatial sampling rate to use
>>
>> other journal
>>
>> reviewer 2:
>> ..a pipeline for speckle counting on the CellProfiler example page that
>> seems relevant...
>> and..the use of passive voice throughout makes it a difficult and dry
>> read..
>>
>> reviewer 3:
>>
>> The authors fail to demonstrate that using this method increases the
>> accuracy of their
>> quantitation (We were aiming at preserving the accuracy and minimizing the
>> effort!!).
>>
>> This method is not broadly applicable (???, almost  every lab has to
>> quantify images).
>>
>> My main idea behind submitting the manuscript was, that its always nice to
>> have an
>> example of a working protocol, and sampling rate is something often
>> neglected (see
>> comments from reviewer 1). I have seen tons of very smart grad students,
>> who need to
>> do quantification, but end up performing manual counting on their images,
>> since adapting
>> existing protocols is beyond their available effort. On the other hand, I
>> am personally not
>> qualified to go deep into physics and math behind sampling according to
>> the PSF of the
>> system vs sampling based on object density. However, I know that sampling
>> below
>> Nyquist is hot in medical imaging field now.
>>
>> I can not publish the full method within the main paper from the study.
>> Quit? Try other
>> microscopy journals? Publish on the Core's webpage?
>>
>

--
Kurt Thorn
Associate Professor
Director, Nikon Imaging Center
http://thornlab.ucsf.edu/
http://nic.ucsf.edu/blog/

[Michael Giacomelli]

*****
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Post images on http://www.imgur.com and include the link in your posting.
*****

Biomedical Optics Express

Mike

On Wed, May 20, 2015 at 12:16 PM, Kurt Thorn <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> I would also look at PLoS One - they are not supposed to evaluate on
> impact, just on scientific correctness.  The one paper I published there
> was a fairly easy process. It is open access with publishing charges.
>
> Kurt
>
>
> On 5/20/2015 8:22 AM, Craig Brideau wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Have you considered an Engineering journal like SPIE Biophotonics? They
>> might be more appreciative of a sampling technique, and since they went
>> open access their impact factor has started to climb a bit. It was fairly
>> exclusive before going open.
>>
>> Craig
>> On May 20, 2015 8:32 AM, "Maria Y. Boulina" <[hidden email]> wrote:
>>
>>  *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> Post images on http://www.imgur.com and include the link in your
>>> posting.
>>> *****
>>>
>>> Folks,
>>>
>>> I need your advice on what to do with a manuscript. The story is, we have
>>> been working
>>> on a quantification protocol for a while with a student on her
>>> large-scale
>>> imaging project.
>>> We spent some brain power on it, so at the end, we have decided to
>>> publish
>>> it as a small
>>> methods paper. the novelty of our approach was applying the Nyquist
>>> sampling rate to
>>> the target object size, rather than the confocal system output AND
>>> adequate post-
>>> processing. we have shown that 1)our suggested algorithm works well in
>>> terms of
>>> preserving the number of counts acquired, compared to higher sampling
>>> rates; and allows
>>> to  keep image size/sampling density/imaging time about several fold
>>> lower
>>> than you
>>> would do standard 2)if you neglect proper sampling rates (linked to the
>>> object size!) or
>>> skip processing, your results suck.
>>>
>>> we have sent the paper to two journals, and received three sets of
>>> comments
>>>
>>> reviewer 1: overall correct, but...nothing new .. AND(!!)... In many
>>> studies,
>>> photobleaching is a major determinant of the spatial sampling rate to use
>>>
>>> other journal
>>>
>>> reviewer 2:
>>> ..a pipeline for speckle counting on the CellProfiler example page that
>>> seems relevant...
>>> and..the use of passive voice throughout makes it a difficult and dry
>>> read..
>>>
>>> reviewer 3:
>>>
>>> The authors fail to demonstrate that using this method increases the
>>> accuracy of their
>>> quantitation (We were aiming at preserving the accuracy and minimizing
>>> the
>>> effort!!).
>>>
>>> This method is not broadly applicable (???, almost  every lab has to
>>> quantify images).
>>>
>>> My main idea behind submitting the manuscript was, that its always nice
>>> to
>>> have an
>>> example of a working protocol, and sampling rate is something often
>>> neglected (see
>>> comments from reviewer 1). I have seen tons of very smart grad students,
>>> who need to
>>> do quantification, but end up performing manual counting on their images,
>>> since adapting
>>> existing protocols is beyond their available effort. On the other hand, I
>>> am personally not
>>> qualified to go deep into physics and math behind sampling according to
>>> the PSF of the
>>> system vs sampling based on object density. However, I know that sampling
>>> below
>>> Nyquist is hot in medical imaging field now.
>>>
>>> I can not publish the full method within the main paper from the study.
>>> Quit? Try other
>>> microscopy journals? Publish on the Core's webpage?
>>>
>>>
>>
>
> --
> Kurt Thorn
> Associate Professor
> Director, Nikon Imaging Center
> http://thornlab.ucsf.edu/
> http://nic.ucsf.edu/blog/
>

[ANDREW EISENHAWER]

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*****


   
Is the method too much to link as supplemental info on the main project paper?
That alone might increase them impact of the project paper.



Sent from my Samsung device over Bell's LTE network.

-------- Original message --------
From: Michael Giacomelli <[hidden email]>
Date: 05-20-2015  12:05 PM  (GMT-07:00)
To: [hidden email]
Subject: Re: advice wanted

*****
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*****

Biomedical Optics Express

Mike

On Wed, May 20, 2015 at 12:16 PM, Kurt Thorn <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> I would also look at PLoS One - they are not supposed to evaluate on
> impact, just on scientific correctness.  The one paper I published there
> was a fairly easy process. It is open access with publishing charges.
>
> Kurt
>
>
> On 5/20/2015 8:22 AM, Craig Brideau wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Have you considered an Engineering journal like SPIE Biophotonics? They
>> might be more appreciative of a sampling technique, and since they went
>> open access their impact factor has started to climb a bit. It was fairly
>> exclusive before going open.
>>
>> Craig
>> On May 20, 2015 8:32 AM, "Maria Y. Boulina" <[hidden email]> wrote:
>>
>>  *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> Post images on http://www.imgur.com and include the link in your
>>> posting.
>>> *****
>>>
>>> Folks,
>>>
>>> I need your advice on what to do with a manuscript. The story is, we have
>>> been working
>>> on a quantification protocol for a while with a student on her
>>> large-scale
>>> imaging project.
>>> We spent some brain power on it, so at the end, we have decided to
>>> publish
>>> it as a small
>>> methods paper. the novelty of our approach was applying the Nyquist
>>> sampling rate to
>>> the target object size, rather than the confocal system output AND
>>> adequate post-
>>> processing. we have shown that 1)our suggested algorithm works well in
>>> terms of
>>> preserving the number of counts acquired, compared to higher sampling
>>> rates; and allows
>>> to  keep image size/sampling density/imaging time about several fold
>>> lower
>>> than you
>>> would do standard 2)if you neglect proper sampling rates (linked to the
>>> object size!) or
>>> skip processing, your results suck.
>>>
>>> we have sent the paper to two journals, and received three sets of
>>> comments
>>>
>>> reviewer 1: overall correct, but...nothing new .. AND(!!)... In many
>>> studies,
>>> photobleaching is a major determinant of the spatial sampling rate to use
>>>
>>> other journal
>>>
>>> reviewer 2:
>>> ..a pipeline for speckle counting on the CellProfiler example page that
>>> seems relevant...
>>> and..the use of passive voice throughout makes it a difficult and dry
>>> read..
>>>
>>> reviewer 3:
>>>
>>> The authors fail to demonstrate that using this method increases the
>>> accuracy of their
>>> quantitation (We were aiming at preserving the accuracy and minimizing
>>> the
>>> effort!!).
>>>
>>> This method is not broadly applicable (???, almost  every lab has to
>>> quantify images).
>>>
>>> My main idea behind submitting the manuscript was, that its always nice
>>> to
>>> have an
>>> example of a working protocol, and sampling rate is something often
>>> neglected (see
>>> comments from reviewer 1). I have seen tons of very smart grad students,
>>> who need to
>>> do quantification, but end up performing manual counting on their images,
>>> since adapting
>>> existing protocols is beyond their available effort. On the other hand, I
>>> am personally not
>>> qualified to go deep into physics and math behind sampling according to
>>> the PSF of the
>>> system vs sampling based on object density. However, I know that sampling
>>> below
>>> Nyquist is hot in medical imaging field now.
>>>
>>> I can not publish the full method within the main paper from the study.
>>> Quit? Try other
>>> microscopy journals? Publish on the Core's webpage?
>>>
>>>
>>
>
> --
> Kurt Thorn
> Associate Professor
> Director, Nikon Imaging Center
> http://thornlab.ucsf.edu/
> http://nic.ucsf.edu/blog/
>

[Cole, Richard W (HEALTH)]

*****
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*****

As an editor of the JOURNAL OF BIOMOLECULAR TECHNIQUES (JBT)  http://jbt.abrf.org I would be happy to look at your manuscript.  
JBT is a peer review journal associated with The Association of Biomolecular Resource Facilities ( an organization made-up largely of core personnel)

Best of luck

Rich


Richard Cole
Research Scientist V
Director: Advanced Light Microscopy & Image Analysis Core
Wadsworth Center
 
Research Assistant Professor
Dept. of Biomedical Sciences
School of Public Health State University of New York

P.O. Box 509 Albany N.Y. 12201-0509
518-474-7048 Phone
518-486-2693 Fax

Website www.wadsworth.org/cores/alm/index.htm

[Maria Y. Boulina]

*****
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Post images on http://www.imgur.com and include the link in your posting.
*****

Nuno,
Thank you!

2015-05-20 10:59 GMT-04:00 Nuno Moreno <[hidden email]>:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear Maria
>
> Its is true that there is little room for methodologies developed in core
> facilities. They might be of great value for the community but
> scientifically not so relevant or new.
>
> This was one of the reasons why we just release an award targeting exactly
> this kind of work. The award has international and independent reviewers.
> Therefore, on top of the prize (a macbook for you and our software for 2
> years for your institution), there is also the international recognition.
>
> More details at
> cirklo.org  (follow the prize link)
>
> Good luck with your application!
>
> All the best
> Nuno Moreno
>
> > On 20 May 2015, at 15:30, Maria Y. Boulina <[hidden email]> wrote:
> >
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > Post images on http://www.imgur.com and include the link in your
> posting.
> > *****
> >
> > Folks,
> >
> > I need your advice on what to do with a manuscript. The story is, we
> have been working
> > on a quantification protocol for a while with a student on her
> large-scale imaging project.
> > We spent some brain power on it, so at the end, we have decided to
> publish it as a small
> > methods paper. the novelty of our approach was applying the Nyquist
> sampling rate to
> > the target object size, rather than the confocal system output AND
> adequate post-
> > processing. we have shown that 1)our suggested algorithm works well in
> terms of
> > preserving the number of counts acquired, compared to higher sampling
> rates; and allows
> > to  keep image size/sampling density/imaging time about several fold
> lower than you
> > would do standard 2)if you neglect proper sampling rates (linked to the
> object size!) or
> > skip processing, your results suck.
> >
> > we have sent the paper to two journals, and received three sets of
> comments
> >
> > reviewer 1: overall correct, but...nothing new .. AND(!!)... In many
> studies,
> > photobleaching is a major determinant of the spatial sampling rate to use
> >
> > other journal
> >
> > reviewer 2:
> > ..a pipeline for speckle counting on the CellProfiler example page that
> seems relevant...
> > and..the use of passive voice throughout makes it a difficult and dry
> read..
> >
> > reviewer 3:
> >
> > The authors fail to demonstrate that using this method increases the
> accuracy of their
> > quantitation (We were aiming at preserving the accuracy and minimizing
> the effort!!).
> >
> > This method is not broadly applicable (???, almost  every lab has to
> quantify images).
> >
> > My main idea behind submitting the manuscript was, that its always nice
> to have an
> > example of a working protocol, and sampling rate is something often
> neglected (see
> > comments from reviewer 1). I have seen tons of very smart grad students,
> who need to
> > do quantification, but end up performing manual counting on their
> images, since adapting
> > existing protocols is beyond their available effort. On the other hand,
> I am personally not
> > qualified to go deep into physics and math behind sampling according to
> the PSF of the
> > system vs sampling based on object density. However, I know that
> sampling below
> > Nyquist is hot in medical imaging field now.
> >
> > I can not publish the full method within the main paper from the study.
> Quit? Try other
> > microscopy journals? Publish on the Core's webpage?
>

[Maria Y. Boulina]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Thank you Craig, Kurt, Michael, Cristina, Andrew and Cole!! We will  shape
our strategy based on your suggestions!
Thanks again,
Marcia

2015-05-20 11:22 GMT-04:00 Craig Brideau <[hidden email]>:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Have you considered an Engineering journal like SPIE Biophotonics? They
> might be more appreciative of a sampling technique, and since they went
> open access their impact factor has started to climb a bit. It was fairly
> exclusive before going open.
>
> Craig
> On May 20, 2015 8:32 AM, "Maria Y. Boulina" <[hidden email]> wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > Post images on http://www.imgur.com and include the link in your
> posting.
> > *****
> >
> > Folks,
> >
> > I need your advice on what to do with a manuscript. The story is, we have
> > been working
> > on a quantification protocol for a while with a student on her
> large-scale
> > imaging project.
> > We spent some brain power on it, so at the end, we have decided to
> publish
> > it as a small
> > methods paper. the novelty of our approach was applying the Nyquist
> > sampling rate to
> > the target object size, rather than the confocal system output AND
> > adequate post-
> > processing. we have shown that 1)our suggested algorithm works well in
> > terms of
> > preserving the number of counts acquired, compared to higher sampling
> > rates; and allows
> > to  keep image size/sampling density/imaging time about several fold
> lower
> > than you
> > would do standard 2)if you neglect proper sampling rates (linked to the
> > object size!) or
> > skip processing, your results suck.
> >
> > we have sent the paper to two journals, and received three sets of
> comments
> >
> > reviewer 1: overall correct, but...nothing new .. AND(!!)... In many
> > studies,
> > photobleaching is a major determinant of the spatial sampling rate to use
> >
> > other journal
> >
> > reviewer 2:
> > ..a pipeline for speckle counting on the CellProfiler example page that
> > seems relevant...
> > and..the use of passive voice throughout makes it a difficult and dry
> > read..
> >
> > reviewer 3:
> >
> > The authors fail to demonstrate that using this method increases the
> > accuracy of their
> > quantitation (We were aiming at preserving the accuracy and minimizing
> the
> > effort!!).
> >
> > This method is not broadly applicable (???, almost  every lab has to
> > quantify images).
> >
> > My main idea behind submitting the manuscript was, that its always nice
> to
> > have an
> > example of a working protocol, and sampling rate is something often
> > neglected (see
> > comments from reviewer 1). I have seen tons of very smart grad students,
> > who need to
> > do quantification, but end up performing manual counting on their images,
> > since adapting
> > existing protocols is beyond their available effort. On the other hand, I
> > am personally not
> > qualified to go deep into physics and math behind sampling according to
> > the PSF of the
> > system vs sampling based on object density. However, I know that sampling
> > below
> > Nyquist is hot in medical imaging field now.
> >
> > I can not publish the full method within the main paper from the study.
> > Quit? Try other
> > microscopy journals? Publish on the Core's webpage?
> >
>

[Neil Kad]

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Dear All,

 

I have a position for a postdoc in my
lab to implement and optimize a multi-colour simultaneous wide-field imaging system. Once functional this system will be used to follow multiple components involved in DNA repair at the single molecule level.  
The University of Kent is less than one hour by train from St. Pancras station in central London, so although this is a one-year position it is commutable for someone already living in/around London.
 If you are interested take a look at the link below or if you know of someone else that might be interested please pass on
this email.  

The University of Kent
vacancies page:  http://tinyurl.com/kad-lab


An overview of the position on my lab website: http://kadlab.mechanicsanddynamics.com/index.php/join-us

Cheers,

 

Neil




=================================

Neil M. Kad PhD.,

School of
Biosciences,

University of Kent,

Canterbury,

Kent CT2 7NH,

United Kingdom.

 

Tel: [phone]
816151

http://kadlab.mechanicsanddynamics.com/

=================================