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16:07, 6 August 2019
Methods for validating OME-XML files
''How do I open/read my metadata?'' =
To start, try a high level API approach via a GUI...
=== Using a GUI ===
If importing your images via [https://imagej.net/Bio-Formats#Bio-Formats_Importer Bio-Formats Importer] (which we suggest you do), you can either:
* In '''Stack Viewing''', View stack with: "Metadata only"
* In '''Metadata viewing''': check "Display Metadata" or "Display OME-XML metadata"
[[OMEVisual]] is another tool that can visualize OME metadata; it is a [[Fiji]] plugin.
These tools allow you to quickly check if your metadata 'looks' correct... are there the correct number of image blocks (i.e. one per tile if multi-scan image)? Are the dimensions correct? etc.
= ''What if I cannot read my metadata via a GUI?!'' =
Did you observe a problem with your metadata via a GUI? Was there no data at all? Or was metadata missing? If this is the case, then perhaps there are structural issues with your metadata that require a bit more in-depth inspection via command line tools.
=== Using the Command Line ===
Bio-Formats has a whole host of information regarding extracting, processing, and validating OME-XML. So check out [https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/tools.html their resources]
more detailed information.
In brief, there are a host of [https://docs.openmicroscopy.org/bio-formats/6.2.0/users/comlinetools/ command line tools available via Bio-Formats] to properly inspect and validate the XML in an OME-TIFF file.
Both the <code>tiffcomment</code> and <code>xmlvalid</code> commands are used; <code>tiffcomment</code> extracts the XML from the file and <code>xmlvalid</code> validates the XML and prints any errors to the console. See [https://docs.openmicroscopy.org/bio-formats/6.2.0/users/comlinetools/
-validation.html this page] for more details.
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