ScanImage Tiff Files

ScanImage records images, volumes and video as Tiff or BigTiff files. For the most part Tiff and BigTiff are similar, but they are not the same; BigTiff enables storage of larger (>4GB) data sets. In addition to the image data, ScanImage stores metadata describing the microscope configuration and settings used during the acquisition. These are stored in the file itself.

Some of this metadata is accessible using standard Tiff readers. The tiff format provides for data fields (tags) which can be used to attach data to describing each frame. Past versions of ScanImage would store a copy the metadata in “image description” tag for each frame. Much of the metadata is redundant, and this can lead to longer load times and significant storage overhead in some cases.

Fortunately, the tiff format is very flexible and allows us to easily store the part of the metadata that doesn’t change over time in a dedicated block of the file. However, this metadata block is only accessible if you know where to look. The tiff files can still be read by any reader conforming to the baseline tiff specification, but those readers will not be aware of the ScanImage metadata block. The ScanImageTiffReader knows how to extract this metadata and also provides fast access to the images themselves.

ScanImage tiff files store the following kinds of data:

Kind Description
data The image data itself
metadata Frame-invariant metadata such as the microscope configuration and region of interest descriptions.
descriptions Frame-varying metadata such as timestamps and I2C data.

The metadata sections themselves are encoded as either matlab evaluable strings or json.

The ScanImage documentation has a very detailed description of how data is stored in a ScanImage Tiff.