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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>Ilya,
and all,<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'>First
of all thanks a lot for all the kind help so far. Even though the progress is
very slow (due to my lack of time) I believe I made some substantial progress
thanks to your kind help.<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'>I
just wanted to clarify a few things when implementing the INCell importer:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt'>The
way GE/Amersham handles the information from their INCell 3000 is to store
information about a screen in a file called “run”-file. This file
would contain information about the number of plates, which lasers where used,
what the plates where named and basically anything that is true for all images
from that screen. Images are stored in sub-directories; each plate having its
own sub-directory. Then there can be several other sub-directories with addition
information that is not that important. At some point I would also like to be
able to read in the information from the automated and semi-automated analyses
that can be done with the INCell software, which are stored in some of those
subdirectories (but this we will do later… ;-).<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'>I
would store the information from the “run”-files on the dataset
level and come up with additional attributes on the dataset level to store that
information.<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 style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face=Wingdings><span style='font-size:10.0pt;font-family:Wingdings'><span
style='mso-list:Ignore'>ð<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'>How do I access those attributes? I would
do it from the importGroup function (that I have to write) using the
newAttribute function ( I will look through a few examples to find a clue on
how to do that, so far I have only seen attributes for images…).<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=Wingdings><span style='font-size:10.0pt;font-family:Wingdings'><span
style='mso-list:Ignore'>ð<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'>How should I distinguish between
different plates? Would this be a dataset underneath a dataset or a parallel dataset?
I could probably also create different new datasets from the run-file and link
later the images to those dataset. How would I do this the best way? <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=Wingdings><span style='font-size:10.0pt;font-family:Wingdings'><span
style='mso-list:Ignore'>ð<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'>Since all the information about a dataset
is in a run-file, I would like to remove all other files from the list and therefore
allow only one file (the run-file) to be in the list at the beginning. Would
this be OK? This would mean that the “run”-files have to be
processed first…<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'>In the
getGroups function I would then add all the images (frm-files) to the list. <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 style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face=Wingdings><span style='font-size:10.0pt;font-family:Wingdings'><span
style='mso-list:Ignore'>ð<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'>Should I modify the attributes of the
dataset already in the getGroups function? This would make my life easier when
importing the frm images, because I can then remove even the run-file from the
file list (no need for an importGroups function) and do the rest of the work in
the frm 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'>The
run-file “knows” about the images and where they are stored (also which
colors where used, which is very important for converting them into any other
format) and thanks to Ilya we now know also the path so we can add the
additional images.<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 style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo3'><![if !supportLists]><font
size=2 face=Wingdings><span style='font-size:10.0pt;font-family:Wingdings'><span
style='mso-list:Ignore'>ð<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'>How do I add image files (frm files) to
the file list? I use upload (as Ilya said) but then I don’t know how to
register the connection in the “regular” way and I don’t see
the new file being processed (I guess this has something to do with the
registration).<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=2 face=Arial><span style='font-size:10.0pt'>Well
I guess that’s enough for now…<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
for your input.<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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