What is metadata?
When acquiring images in microscopy, the image files that are stored contain two main things:
- image data: which is essentially ‘pixel values’
- 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 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 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.
