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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Hello
again,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Yet another
issue: The INCell analyzer comes with software to analyze the images it
creates. It can analyze the images on the fly and also off-line. The results
are stored (of course) in the same directory structure with different
subfolders for all the analyses. Each analysis file is a text file with a
header section describing the user who performed the analysis, which module was
used and the parameters used. The last part of the file contains CSV list with
a header line and lots of numbers afterwards (some of them actually mean
something).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Some
of the issues I see are that the only reliable way to link the data is through
the directory structure. The spreadsheet importer needs images IDs that have to
be obtained from OME so a simple script to reformat the results file wouldn’t
work.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Now I
thought of four possible scenarios on how to get this information into OME:<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt'><span style='mso-list:Ignore'>a)<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2><span
style='font-size:10.0pt'>First run the importer on the “run” file. Within
this procedure a file that knows how to link image ID’s with analysis
results will be created. Then execute a script that combines the information.
Then use the spreadsheet importer.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo3'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt'><span style='mso-list:Ignore'>a.<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2><span
style='font-size:10.0pt'>This is too difficult and there are too many steps
involved = not a good solution<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt'><span style='mso-list:Ignore'>b)<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2><span
style='font-size:10.0pt'>Write an importer for the analysis files. This would “somehow”
use the directory structure to identify the screen, plates and wells, i.e. images
to import the results<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo3'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt'><span style='mso-list:Ignore'>a.<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2><span
style='font-size:10.0pt'>This has the advantage that the images wouldn’t
be read in again (see c)). This “somehow” would mean that the
directory would have to be stored in OME. And I guess it will be a bit unsafe
(what happens if the analysis files resides somewhere where it doesn’t
belong???<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt'><span style='mso-list:Ignore'>c)<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2><span
style='font-size:10.0pt'>Import the results together with the “run”
file.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo3'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt'><span style='mso-list:Ignore'>a.<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2><span
style='font-size:10.0pt'>Probably the best solution, but this would mean that
if someone reanalyzed the images, everything had to be re-imported, images had
to be uncompressed again (this takes a <st1:place w:st="on">LOT</st1:place> of
time)…<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt'><span style='mso-list:Ignore'>d)<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2><span
style='font-size:10.0pt'>Lastly after reading about HTML templates I thought
one could create a web-page to link a screen or plate with a specific analysis
file<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo3'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt'><span style='mso-list:Ignore'>a.<font
size=1 face="Times New Roman"><span style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2><span
style='font-size:10.0pt'>Well here I have absolutely no clue how to do it, but
it would fit my way of thinking in terms of making it easier to link additional
information to already existing data. Maybe one could actually generalize this
to build a structure like for the image importer but this time only for linked
information. Or do you believe that is already done with the spreadsheet
importer???<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Or,
maybe one could combine a) and d)???<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Please
advise!!!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Thanks<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Bernd<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p><font size=2 face="Times New Roman"><span style='font-size:10.0pt'>Bernd
Jagla, PhD<br>
Associate Research Scientist<br>
<st1:place w:st="on"><st1:PlaceName w:st="on">Columbia</st1:PlaceName> <st1:PlaceType
w:st="on">University</st1:PlaceType></st1:place><br>
<st1:Street w:st="on"><st1:address w:st="on">1150 St. Nicholas Avenue</st1:address></st1:Street><br>
Russ Berrie Medical Pavilion, Room 520<br>
<st1:place w:st="on"><st1:City w:st="on">New York</st1:City>, <st1:State w:st="on">NY</st1:State>
<st1:PostalCode w:st="on">10032</st1:PostalCode></st1:place><br>
Tel: 212 - 851 5560 x16<br>
Fax: 212 - 851 5570<br>
e-mail: baj2107@columbia.edu<br>
</span></font> <o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
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