Difference between revisions of "Metadata"

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To start, try a high level API approach via a GUI...
 
To start, try a high level API approach via a GUI...
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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.
 
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?!'' =
 
= ''What if I cannot read my metadata via a GUI?!'' =
  

Revision as of 10:32, 7 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.