Hi Guenter,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Sorry, I should have been more precise: My
microscope is a home-built light sheet microscope (optically a type of
wide field microscope) with different mechanical, electronic and
optical components, controlled by a PC. Some of the components
obviously are addressed neither by TIFF tags nor by OME-XML scheme tags.<br><br>Basically,
I want to store as many microscope and recording parameters as possible
in appropriate TIFF tags, and additional metadata (plus copies of the
TIFF tags) in a format which is not proprietary but open and expandable
(OME-TIFF / XML seems quite a good candidate). <br><br>First I want to
evaluate the metadata tags already addressed by TIFF as well as by the
OME XML scheme (trying to avoid "private" data tags). <br></blockquote><div><br>Since TIFF is not a microscopy format, I doubt many of the fields you need will be available. However, most of the microscopy-specific fields you need should be available in the OME schema. If not, we are enthusiastic about expanding the specification to accommodate additional needs; just let us know which specific fields you are considering. For extremely niche metadata fields, you can use a feature of OME-XML called structured annotations to represent the information in a semi-structured way.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Other
metadata (many still to be defined) may then in addition be stored as
(preliminary) XML tags (sometimes hopefully making it into a common,
open scheme, or finding their equivalent in it).<br></blockquote><div><br>Indeed, the goal is for OME-XML to be able to express the majority of people's use cases for microscopy metadata.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Did I miss something, or is there a better way to proceed?</blockquote><div><br>What my group did (LOCI) with our home-built systems is to add support for OME-TIFF to our internal acquisition software. To accomplish this, we use Bio-Formats (<a href="http://www.loci.wisc.edu/ome/formats.html">http://www.loci.wisc.edu/ome/formats.html</a>) with Ice, to harness the Bio-Formats metadata API, and embed OME-XML into our TIFFs using libtiff. There is a brief, somewhat out of date overview at:<br>
<br> <a href="http://www.loci.wisc.edu/ome/wiscscan.html">http://www.loci.wisc.edu/ome/wiscscan.html</a><br><br>Did you also create your own acquisition package, or are you using an off-the-shelf program?<br><br>Lastly, we are almost finished with a C++ wrapper that should make Bio-Formats easier to use from within acquisition software.<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> <a href="https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader" target="_blank">https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader</a><br>
<br></div>Thanks, this is exactly the stuff I was looking for. I will check in more detail tomorrow.<br></blockquote><div><br>Let me know if you have any questions.<br><br>To caution you, the fields listed on that wiki are a subset of all available OME-XML fields. They represent only those currently mapped by Bio-Formats into our flat metadata API. However, it is quite easy for us to map in additional fields from the XML schema into Bio-Formats. I can elaborate further on this process if you are interested.<br>
<br>For a full list of all available OME metadata, see:<br><br> <a href="https://openmicroscopy.org/Schemas/OME/2008-09/ome.xsd">https://openmicroscopy.org/Schemas/OME/2008-09/ome.xsd</a><br><br>And for further documentation:<br>
<a href="https://openmicroscopy.org/Schemas/">https://openmicroscopy.org/Schemas/</a><br> <a href="http://ome-xml.org/browser/Documentation">http://ome-xml.org/browser/Documentation</a><br> <a href="http://ome-xml.org/">http://ome-xml.org/</a><br>
<br>There are other diagrams as well but I don't have the URLs handy at the moment.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I
am not a programmer (others are in charge of this), but highly
concerned about proper metadata storage handling, and retrieval of
course. I have been struggling, as a microscopy facility manager, with
the mess of proprietary (or simply non-existing) metadata since years.
I hope an open standard (like OME-TIFF / XML) will meet my demands. <br></blockquote></div><br>Join the club. :-) The OME data model exists for people in positions like yours, so please let us know if it does not meet your needs!<br>
<br>Regards,<br>-Curtis<br><br><div class="gmail_quote">On Wed, Mar 11, 2009 at 4:21 PM, Guenter Giese <span dir="ltr"><<a href="mailto:Guenter.Giese@mpimf-heidelberg.mpg.de" target="_blank">Guenter.Giese@mpimf-heidelberg.mpg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Curtis,<br><br>thank you for your rapid answer! It addresses my questions almost perfectly. <br>
<div><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I am not sure what you mean by "microscopy-related TIFF tags." There are many proprietary microscopy-specific variants of TIFF (e.g.: Flex, Olympus Fluoview, Molecular Dynamics GEL, Imaris, Improvision, Metamorph, Nikon, Image-Pro Sequence, SVS, Zeiss LSM) that contain extra information, but these are not OME-TIFFs. However, Bio-Formats parses each format's proprietary metadata and converts what it can into OME-XML.<br>
<br><br></div>Sorry, I should have been more precise: My microscope is a home-built light sheet microscope (optically a type of wide field microscope) with different mechanical, electronic and optical components, controlled by a PC. Some of the components obviously are addressed neither by TIFF tags nor by OME-XML scheme tags.<br>
<br>Basically, I want to store as many microscope and recording parameters as possible in appropriate TIFF tags, and additional metadata (plus copies of the TIFF tags) in a format which is not proprietary but open and expandable (OME-TIFF / XML seems quite a good candidate). <br>
<br>First I want to evaluate the metadata tags already addressed by TIFF as well as by the OME XML scheme (trying to avoid "private" data tags). <br><br>Other metadata (many still to be defined) may then in addition be stored as (preliminary) XML tags (sometimes hopefully making it into a common, open scheme, or finding their equivalent in it).<br>
<br><br>Did I miss something, or is there a better way to proceed?<div><br><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>For example, if you mouse over the entry for TIFF, at the bottom of the pop-up you will see a link to "Supported metadata fields":<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> <a href="https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader" target="_blank">https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader</a><br>
<br></div>Thanks, this is exactly the stuff I was looking for. I will check in more detail tomorrow.<br><br><br>I am not a programmer (others are in charge of this), but highly concerned about proper metadata storage handling, and retrieval of course. I have been struggling, as a microscopy facility manager, with the mess of proprietary (or simply non-existing) metadata since years. I hope an open standard (like OME-TIFF / XML) will meet my demands. <br>
<div><div></div><div> <br><br>Best,<br><br>Guenter<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> ------------------------------------------<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Dr. Guenter Giese<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Light Microscopy Facility Manager<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Dept. of Biomedical Optics<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> MPI fuer Medizinische Forschung Jahnstr. 29<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> D-69120 Heidelberg, Germany<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Phone (+49) 6221-486-360 (Fax: -325)<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> e-mail: <a>guenter.giese@mpimf-heidelberg.mpg.de</a><br>
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