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Biomedical Optics Express

Mike

On Wed, May 20, 2015 at 12:16 PM, Kurt Thorn <[log in to unmask]> wrote:

> *****
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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" <[log in to unmask]> 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/
>