Difference between revisions of "Metadata"

(What is metadata?: minor edits)
(Methods for validating OME-XML files)
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= Methods for validating xml files =
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= ''How do I open/read my metadata?'' =
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To start, try a high level API approach via a GUI...
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=== Using a GUI ===
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If importing your images via [https://imagej.net/Bio-Formats#Bio-Formats_Importer Bio-Formats Importer] (which we suggest you do), you can either:
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* In '''Stack Viewing''', View stack with: "Metadata only"
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OR
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* In '''Metadata viewing''': check "Display Metadata" or "Display OME-XML metadata"
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[[OMEVisual]] is another tool that can visualize OME metadata; it is a [[Fiji]] plugin.
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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.
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= ''What if I cannot read my metadata via a GUI?!'' =
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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.
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=== Using the Command Line ===
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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 more detailed information.
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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.
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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-validation.html this page] for more details.

Revision as of 16:07, 6 August 2019


What is metadata?

When acquiring images in microscopy, the image files that are stored contain two main things:

  1. image data: which is essentially 'pixel values'
  2. metadata: information on the image data including pixel size, bit depth, dimension and objective information, etc.

Metadata is essential to correctly read image data; for example, to have accurate measurements, the image needs to be calibrated according to the correct/associated pixel size. Saving and preserving metadata is key in quantitative image analysis.

How can I see my image's metadata?

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 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 their resources for more detailed information.

In brief, there are a host of command line tools available via Bio-Formats to properly inspect and validate the XML in an OME-TIFF file.

Both the tiffcomment and xmlvalid commands are used; tiffcomment extracts the XML from the file and xmlvalid validates the XML and prints any errors to the console. See this page for more details.