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Task #12473 (new)

Opened 5 years ago

Last modified 5 years ago

Channel should model separate probe/fluor metadata attributes

Reported by: rleigh Owned by: rleigh
Priority: minor Milestone: Unscheduled
Component: Specification Version: 5.0.2
Keywords: schema Cc: forrest.collman@…, mlinkert
Resources: n.a. Referenced By: https://trello.com/c/cFdEELlG/43-description-attribute-on-channel-and-other-elements-with-name-attribute
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by rleigh)

Most users and indeed file formats aren't separating the conjugated probes into separate metadata elements, so for most cases the existing channel name is sufficient for these needs. However, newer formats like CZI do allow separation of the conjugated fluorophore and the probe.

With the current model, the channel name might be a physical hardware parameter (channel ID or filter name) or a general name e.g. CK18-AF594 where with CZI we have a name plus a description. You could separate the probe (anti-cytokeratin-18) from its flurophore (Alexa
Fluor 594). However, CZI's use of channel name and description for modelling this isn't particularly self-describing. We might want to retain the generic channel name and provide additional attributes for the probe and the reporter (which isn't necessarily fluorescent), and possibly also have another generic "description" attribute for detailed description.

Also note that there isn't necessarily a 1:1 correspondence between channel and probe/fluor. Examples include hyperspectral imaging and normal imaging which requires correction for "bleedthrough" between channels. In these cases, the physical channels used for acquisition require transformation to a set of logical channels which will be equal to or less than the acquisition channel count in number. We might want to consider modelling this as part of the rendering settings work, or possibly split it out as a separate unit of work.

Modelling suggestions:

  • physical channel ID (hardware channel ID/name)
  • logical channel ID (post-correction/unmixing ID/name)
  • reporter (attach to logical channel if used, otherwise physical channel)
  • probe (attach to logical channel if used, otherwise physical channel)
  • additional free-text description for use in the absence of specific reporter/probe metadata

Change History (5)

comment:1 Changed 5 years ago by rleigh

  • Description modified (diff)

comment:2 Changed 5 years ago by rleigh

  • Description modified (diff)

comment:3 Changed 5 years ago by mlinkert

  • Cc mlinkert added

comment:4 Changed 5 years ago by mlinkert

See QA 9402.

comment:5 Changed 5 years ago by ajpatterson

  • Keywords schema added
  • Owner changed from ajpatterson to rleigh
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