This article explains what metadata is, why it is important, and how arivis deals with metadata during import and image processing
What is metadata?
Metadata is information about an image.
As explained in this article about what is an image, an image file is essentially a collection of intensity values. However, a list of numbers on its own isn't an image, and in any case, every type of computer file depends on metadata of some sort for the computer to handle the file correctly.
Some metadata is universal to all computer files. this includes things like the size of the file, the date the file was created and last edited, read & write privileges etc. But most file metadata is format specific. A PDF document will include formatting and pagination information, an Excel spreadsheet will include the number and name of worksheets and formulas, and an image file will also have it's own metadata, kept in a different structure depending on the exact file format. JPEGs and TIFF images might well keep the same metadata, but in different locations and with different labels.
So what kind of metadata does an image file typically include?
First, metadata will include a lot of structural information. This includes things like:
- Bit depths of the image
- width and height of the image
- Additional dimensional information concerning time series, z-planes and image sets
In the context of scientific image analysis, some other metadata might also be really important, including:
- pixel dimensions calibrations
- time intervals between timepoints
- exposure parameters
- lens information such as magnification, numerical aperture and refractive indices
- channel information like laser power and emission wavelength
And many more.
Some of those bits of metadata are clearly more important than others when it comes to image analysis. Information like the spatial and temporal calibration are crucial to the correct interpretation and visualisation of the images. Channel colour information and display range parameters are also clearly very useful for visualisation, but have no effect on segmentation results. Information about the name and model of microscope used can be useful for debugging file compatibility issues, but are generally of little interest to image analysts.
The choice of what metadata to include or omit when writing the file is up to the engineering team who creates and maintains the specific file format. Typically this will be down to the company who manufactures the imaging device, or at least down to the engineer who codes the software that controls the various devices connected to an imaging setup.
Most microscopy files include all this metadata, plus device specific information, and arivis has been engineered to read it and store it in the SIS files it creates.
Metadata such as calibration information and channel visualisation options (colours, display range etc) are automatically translated into their equivalent fields in the SIS metadata where possible. Other metadata which is not relevant to the image analysis process is usually kept in a special metadata container with the SIS file.
Finally, arivis will also create and add its own metadata. This includes objects that are created on the image (segments, tracks, ROIS etc), object features (volume, area, intensity etc), but also pipelines a user creates, modification history and others. Not all of this information is kept in the actual SIS file. Particularly, the objects created by a user, either manually or with a pipeline, are stored in a .OBJECTS file that is separate from the SIS file but uses the same name. As an example, here you can see a CZI file and the files created by arivis during the import process
If we transfer the SIS file to another location, it is important to also copy these additional files to ensure that we do not lose any metadata.