30. Imaging Profile¶

An imaging archive stores mass spectra acquired at positions on a sample. The profile adds requirements to a Core archive; it takes nothing away.

30.1 Marking an archive as imaging¶

An archive is an imaging archive when metadata.imaging.is_imaging in mzpeak_index.json is true. An imaging archive MUST meet every requirement on this page.

{ "metadata": { "imaging": { "is_imaging": true } } }

30.2 Pixel positions¶

Pixel positions are columns of the scan metadata table:

• In each row, position_x and position_y MUST be both set or both null. A scan that belongs to a pixel has both set. A scan that belongs to no pixel, such as a calibration scan, has both null.
• The values are indices into the pixel grid. They are not physical coordinates.
• Each column MUST have a column mapping entry naming its term.
• Several scans MAY share one position.

Positions define the image. Terms that describe how the instrument scanned the sample, such as scan pattern or line scan direction, are a record of the acquisition. A reader MUST NOT use them to place pixels.

30.3 Grid geometry¶

Exactly one entry of scan_settings_list MUST describe the pixel grid in its parameters:

• Pixel size is the length of a pixel's edge. It is not an area.
• Pixel size and max dimension MUST carry a unit of length, and SHOULD use micrometre (UO:0000017).
• A writer that cannot determine the pixel size SHOULD omit it.

30.4 Vocabulary¶

An imaging archive MUST declare the imaging vocabulary, IMS, in cv_list. That vocabulary publishes no releases, so its uri MUST name a commit, in the form https://raw.githubusercontent.com/imzML/imzML/<commit hash>/imagingMS.obo:

{
  "id": "IMS",
  "full_name": "Imaging Mass Spectrometry Ontology",
  "uri": "https://raw.githubusercontent.com/imzML/imzML/2c28b05ca297430303627d8c7d192cac1a2b1374/imagingMS.obo",
  "version": "1.1.0"
}

30.5 What a validator checks¶

1. metadata.imaging.is_imaging is true.
2. The scan metadata table has integer columns position_x and position_y, each with a column mapping entry for its term. In every row both are set or both are null, and at least one row has both set.
3. position_z, if present, is an integer column with a column mapping entry for its term.
4. Exactly one scan_settings_list entry carries IMS:1000042 and IMS:1000043, each with an integer value of at least 1.
5. Every pixel size and max dimension present carries a unit of length.
6. cv_list declares IMS with a uri of the form given under 30.4 Vocabulary, with a 40-character commit hash.

30.6 Open items¶