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.

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

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.

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.