NHPatterson / codex-common-acquisition-metadata

Internal standards for acquisition metadata

HuBMAP internal metadata standards that describe microscopy acquisition details for imaging spatial proteomics methods CODEX and ImmunoSABER.

Hints

ChannelID must be specified per cycle (i.e. it resets in each cycle). For example:

{"CycleID": 1, "ChannelID": 1}, 
{"CycleID": 1, "ChannelID": 2},
{"CycleID": 1, "ChannelID": 3},
{"CycleID": 2, "ChannelID": 1},
{"CycleID": 2, "ChannelID": 2},
{"CycleID": 2, "ChannelID": 3}

Almost all numerical values start from 1, except for ExposureTimeMS, NominalMagnification, ResolutionX, ResolutionY, ResolutionZ, TileOverlapX, TileOverlapY.

For more information refer to the experiment_schema.json.