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Prevent users from submitting H&E CZI input files to IF pipeline #352

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philipmac opened this issue Oct 10, 2023 · 0 comments
Open

Prevent users from submitting H&E CZI input files to IF pipeline #352

philipmac opened this issue Oct 10, 2023 · 0 comments
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enhancement New feature or request

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@philipmac
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philipmac commented Oct 10, 2023

The current multichannel IF pipeline only checks file type is .czi, and assumes input is IF (i.e. not H&E).

This leads to unexpected behavior if HE inputs are run.

Fail pipeline upon detection?


if IlluminationType !="Epifluorescence":
   raise Exception

Test for H&E and do the right thing (wrt neuroglancer shader) ?

elif IlluminationType=="Transmitted":
  the.right.thing(do)

Note, the way this pipeline is set up (AFAIK) the only input that can be used (from the perspective of the user) exists in a specially named dir HQ_images.

@annshress annshress added the enhancement New feature or request label Oct 19, 2023
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