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Wed Apr 27 09:54:51 EDT 2011


on this scale before. With regards to a GUI, I would prefer to create one
through a web browser, because of its ease and cross-platform accessibility,
but I am unclear if this will cause problems with accessing the
"client-side" image files. I would also like to make the code modular, so
that our image processing pipeline can be expanded by others in the lab, but
I do not know any strategies for how to organize code or how to implement
version control.

If anyone is particularly interested in this project or helping me I'd enjoy
meeting in person to have a discussion, though email works fine if that is
not an option.
Thanks,
Kyle

P.S. How will I know if anyone replies to this email? Please let me know by
reaching me via karhohs at fas.harvard.edu.

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Hello HCS Community,<br>I am a graduate student whose current project invol=
ves some image processing. I have been brainstorming about how to make the =
software we write more user friendly and am looking for advice and feedback=
 in this regard.<br>


<br>First, consider the description of the current work flow in our lab as =
3 steps:<br>1. Images are captured on a microscope.<br>2. Images are proces=
sed in both Matlab, ImageJ, and Cell Profiler.<br>3. Data from images are v=
isualized in Matlab.<br>


<br>Right now step 2 is rather cumbersome. We do a fair deal of in-line edi=
ting of the m-files to make changes to file names, the path, and variables =
that are image dependent. This can be time consuming and can lead to the in=
troduction of errors in the code, especially since we do not use a version =
control system. Further, we interact with ImageJ and Cell Profiler through =
their respective GUIs to implement methods that can also be done through a =
command line. <br>
<br>My goal is to write a &quot;wrapper&quot; program in Python that itself=
 will have a gui that will prompt users to make the changes to file names, =
path, and variables and also interface with with ImageJ and Cell Profiler, =
so that is not necessary to open these programs. My goal is to create an ap=
plication that makes it easy to implement (and impossible to mess up) the s=
pecific image processing routines we use in lab.<br>
<br>From here I would like to use best practices, but I have never written =
code on this scale before. With regards to a GUI, I would prefer to create =
one through a web browser, because of its ease and cross-platform accessibi=
lity, but I am unclear if this will cause problems with accessing the &quot=
;client-side&quot; image files. I would also like to make the code modular,=
 so that our image processing pipeline can be expanded by others in the lab=
, but I do not know any strategies for how to organize code or how to imple=
ment version control.<br>

<br>If anyone is particularly interested in this project or helping me I&#3=
9;d enjoy meeting in person to have a discussion, though email works fine i=
f that is not an option.<br>
Thanks,<br>Kyle<br><br>P.S. How will I know if anyone replies to this email=
? Please let me know by reaching me via karhohs at <a href=3D"http://fas.ha=
rvard.edu" target=3D"_blank">fas.harvard.edu</a>.<br><div style=3D"padding:=
0px;margin-left:0px;margin-top:0px;overflow:hidden;word-wrap:break-word;col=
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</div>
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30%">
</div>
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x: 9999; padding: 0px; margin-left: 0px; margin-top: 0px; overflow: hidden;=
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ne-height: 130%;" id=3D"avg_ls_inline_popup">
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