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1,789 bytes added, 6 August
Methods for validating OME-XML files
= Methods ''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" OR* 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] for validating 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/xml files =-validation.html this page] for more details.
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