Technical reference

These pages hold every detail: every option, every format, and the exact layout of the result. You do not need them to convert a dataset. For that, start with Install and Your first conversion.

Page	What it covers
Supported formats	How each format is recognised, what it provides, and what is special about each vendor
Command-line options	Every option of the thyra command, with examples
Resampling	How the shared m/z axis is chosen, and how to control it
Output format	Everything inside the .zarr folder, and how to read it in Python
Coordinate systems	How positions in the result relate to the slide and the optical image
Metadata schema	The structured description of each acquisition, and METASPACE export
Writing the metadata document	For other programs that want to write the same description
For tool developers	For tools that read a store: the rules you can rely on, how changes are versioned, and short recipes
Python API	Every function and class you can use from Python
Design decisions	Why each default is what it is, with the measurements behind it
Format notes	Background on reading imzML, PHI ToF-SIMS and Bruker solariX files