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incomplete_fov_check errors out if gold mass not specified or not named Au #473

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alex-l-kong opened this issue Nov 14, 2024 · 0 comments · May be fixed by #474
Open

incomplete_fov_check errors out if gold mass not specified or not named Au #473

alex-l-kong opened this issue Nov 14, 2024 · 0 comments · May be fixed by #474
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@alex-l-kong
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Describe the bug

In bin_extraction.incomplete_fov_check, the gold channel has two hard requirements as defined at https://github.com/angelolab/toffy/blob/main/src/toffy/bin_extraction.py#L105-L107:

  1. It must exist in the panel. If not, then it's assumed the user forgot to add it.
  2. It must be named Au.tiff.

Each requirement has a problem:

  1. Not every cohort extracts gold as a channel. This will especially be the case as more users run MIBIBlue slides.
  2. Not everyone names the gold mass in the cohort Au.

Expected behavior

We should trust that users have specified their panels correctly. The current pipeline extracts every channel that is specified in the panel, so we shouldn't assume Au isn't specified in the panel but also was extracted.

Because of the inconsistent gold naming conventions/presences across cohorts, we also need to explicitly specify extract_intensities as a kwarg or an explicit variable in the extraction notebook for intensity extraction. We can still default it to ["Au", "chan_39"], but users will be able to easily modify as needed.

To Reproduce

Run a cohort with gold not named "Au" or without gold in the panel.

@alex-l-kong alex-l-kong added the bug Something isn't working label Nov 14, 2024
@alex-l-kong alex-l-kong self-assigned this Nov 14, 2024
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