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Make IMC panel optional #6

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jwindhager opened this issue Apr 26, 2021 · 1 comment
Closed

Make IMC panel optional #6

jwindhager opened this issue Apr 26, 2021 · 1 comment
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enhancement New feature or request

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@jwindhager
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In the IMC preprocessing step, do not require the presence of an IMC panel. If none is available, extract the panel from the mcd/schema files or ignore panel creation.
@jwindhager jwindhager added the enhancement New feature or request label Apr 26, 2021
@jwindhager jwindhager added this to the 0.3.4 milestone Apr 26, 2021
@jwindhager jwindhager self-assigned this Apr 26, 2021
@jwindhager
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As discussed with @nilseling, the IMC Segmentation pipeline-compatible "IMC panel" is generated by airlab and further customized by the user. Given that such a panel is not always present (but the metadata is, at least more often than the panel), the current behavior of steinbock should be improved as follows:

  • If an "IMC panel" is provided in the raw data, take this one
  • Otherwise, if .mcd/.schema files are provided, take the panel from the first one
  • If no "IMC panel" is provided, leave the creation of the steinbock panel up to the user

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