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<DIV><SPAN class=067240818-05032008><FONT face="Lucida Sans Unicode"
color=#0000ff size=2>Curtis,</FONT></SPAN></DIV>
<DIV><SPAN class=067240818-05032008><FONT face="Lucida Sans Unicode"
color=#0000ff size=2>Thanks for the info. I will try that
out.</FONT></SPAN></DIV>
<DIV><SPAN class=067240818-05032008><FONT face="Lucida Sans Unicode"
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=067240818-05032008><FONT face="Lucida Sans Unicode"
color=#0000ff size=2>Chris</FONT></SPAN></DIV>
<BLOCKQUOTE style="MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
ctrueden.wisc@gmail.com [mailto:ctrueden.wisc@gmail.com] <B>On Behalf Of
</B>Curtis Rueden<BR><B>Sent:</B> Wednesday, March 05, 2008 11:38
AM<BR><B>To:</B> Wood, Christopher<BR><B>Cc:</B>
ome-users@lists.openmicroscopy.org.uk<BR><B>Subject:</B> Re: [ome-users] zeiss
lsm metadata<BR><BR></FONT></DIV>Hi Chris,<BR><BR>
<DIV class=gmail_quote>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">We
are using OME server and are importing LSM files into OME with
loci-bioformats. Maybe I have missed it, but I would like to have as
much information from the lsm file as possible, i.e., the objective,
filters, laser power, detector gain, etc. Right now we only get basic image
information.<BR></BLOCKQUOTE>
<DIV><BR>The metadata conversion within Bio-Formats is a work in progress.
There are a number of reasons why not everything may not be
converted.<BR><BR>1) For instrument-related metadata, what is present in third
party acquisition formats such as Zeiss LSM is not a complete specification of
the instrument. The OME data model currently has a serious limitation in that
it does not allow the specification of partial information about many types of
objects. As such, Bio-Formats cannot represent the instrument and its settings
within the OME data model. We have plans to extend the specification to allow
for partial information somehow, but are still hashing out the details. Once
the model has been extended, it will be possible for Bio-Formats to convert
the metadata.<BR><BR>2) Once #1 is taken care of, Bio-Formats still needs to
actually recognize the LSM metadata to be converted to OME, and do so. We do
our best to parse everything from LSM in its original organization, but have
probably missed some fields for the OME conversion step. To address this
problem, it would be very helpful if you had a sample LSM with a list of
fields you know are present, and expect to see represented within
OME.<BR><BR>It is also possible that Bio-Formats is converting some of the
information in question, and you just weren't looking in the right place.
;-) Information about the instrument and other non-Image-specific
metadata can be found by clicking the "Image import" link in the top right
box. You should see a series of tables displaying all the metadata that
Bio-Formats pulled in to the OME system.<BR><BR></DIV>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">Is
that possible right now, or would we need get that information from the file
ourselves.<BR></BLOCKQUOTE></DIV><BR>Assuming you check the "Image import"
screen and the information is not present, you would need to access the
information some other way. You can almost certainly use Bio-Formats to do so,
by pulling the information out of its metadata hashtable (which maintains a
list of metadata key/value pairs straight from the file, with no conversion to
OME). As a quick test, you can set up the Bio-Formats command line tools (see
<<A
href="http://www.loci.wisc.edu/ome/formats.html">http://www.loci.wisc.edu/ome/formats.html</A>>)
and run from a console:<BR><BR>showinf myData.lsm -nopix<BR><BR>It should dump
a whole bunch of information about the file, including all the metadata it
parsed in a big list. If you see what you are looking for, then you are
already most of the way there. If you are a *nix scripter, you can grep out
what you want, or if you are a Java programmer you can use the Bio-Formats
API's loci.formats.IFormatReader.getMetadataValue(String) method.<BR><BR>You
can also see what Bio-Formats is converting to the OME data
model:<BR><BR>showinf myData.lsm -nopix -omexml<BR><BR>That will show you a
block of OME-XML that represents all your metadata (without pixels BinData).
If you see the information you want in the regular metadata table, but not
within the OME-XML block, then it is a problem with the OME conversion step as
discussed above. Any comments on specific LSM fields you have that are not
converted, but should be, would be very helpful.<BR><BR>HTH,<BR>Curtis<BR><BR>
<DIV class=gmail_quote>On Mon, Mar 3, 2008 at 4:36 PM, Wood, Christopher
<<A href="mailto:CJW@stowers-institute.org"
target=_blank>CJW@stowers-institute.org</A>> wrote:<BR>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">Hello,<BR><BR>We
are using OME server and are importing LSM files into OME with
loci-bioformats. Maybe I have missed it, but I would like to have as
much information from the lsm file as possible, i.e., the objective,
filters, laser power, detector gain, etc. Right now we only get basic image
information.<BR><BR>Is that possible right now, or would we need get that
information from the file ourselves.<BR><BR>Thanks<BR>Chris
Wood<BR>_______________________________________________<BR>ome-users mailing
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href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"
target=_blank>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</A><BR></BLOCKQUOTE></DIV><BR></BLOCKQUOTE></BODY></HTML>