imzML 1.1.1

The imzML specification was updated to improve standardisation, the details of which are discussed below. The example files were also updated to adhere to the latest specification and were validated using the imzMLValidator.

Pixel size

The major change made is related to the terms defining pixel size. In the controlled vocabulary two sequential terms were defined as pixel size (IMS:1000046) and image shape (IMS:1000047). In some cases, the latter was erroneously used as pixel size y (IMS:1000047). This discrepancy led to different implementations using the same term in different ways.The two terms have been adjusted to avoid ambiguity, resulting in pixel size (x) (IMS:1000046) and pixel size y (IMS:1000047). This adds new functionality to the imzML standard (i.e.,allowing rectangular, but non-square, pixels to be represented)and should be compatible with existing imzMLfiles. In thesituation in which the pixel sizes in the x and y dimensions are equal (which is true in the majority of cases), it is sufficient to only provide the CV parameter pixel size (x) (IMS:1000046).

UUID

In the original specification there were no strict definitions ofthe formats to be used to represent the UUID and hash value in the imzML file. This has led to different implementations, with some imzML exporters including curly braces around the UUID (which is how Microsoft GUIDs are often represented, for example “{1523c65a-4326-401e-9a52-e3326b401871}”), other exporters following the UUID specification directly,20andothers following neither of these with some combination of using curly braces, capital letters, and omitting hyphen separators. Similarly, there is a difference in how some exporters represent the hash value in the imzML file. To ensure consistency, additions to the specification have been made,stating that both the hash and UUID are case insensitive, and the UUID value should be stored using hyphen separators (in the form 8-4-4-4-12) with no curly braces.

Minor schema changes

Additional modifications to the specification, which improve the ability to detect nonsensical imzML files, include making the tags and mandatory. Details about the image display, such as the number of pixels in each dimension and pixel size are stored as parameters within the tag. The tag, which is part of each spectrum, contains the spatial location of each pixel. Previously, both tags were optional and therefore could (theoretically) be omitted, while remaining a technically valid imzML file.