5 Key Takeaways

• 1

  Thyra is an open-source library that converts mass spectrometry imaging data into SpatialData objects for multimodal analysis.

• 2

  The software supports raw vendor files and imzML, harmonizes mass-to-charge axes, and processes datasets larger than available computer memory.

• 3

  Thyra stores ion images, spectra, and pixel coordinates in a shared physical coordinate system and writes outputs in cloud-compatible Zarr v3.

• 4

  The authors demonstrated integration of MSI, hematoxylin and eosin histology, and Xenium spatial transcriptomics in a mouse brain dataset.

• 5

  The authors noted that MSI pixel size, tissue deformation, and image-registration accuracy limit interpretation, and the current release does not preserve ion-mobility data.