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[2.0] Re-organize acquisition around channels #1180

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dbirman opened this issue Dec 6, 2024 · 1 comment
Open
3 tasks

[2.0] Re-organize acquisition around channels #1180

dbirman opened this issue Dec 6, 2024 · 1 comment
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breaking Breaking changes

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@dbirman
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dbirman commented Dec 6, 2024

Is your feature request related to a problem? Please describe.
We want to re-organize acquisition to be organized by imaging channels instead of tiles

Describe the solution you'd like

  • Channel is the main feature of an acquisition
  • Tile deprecated
  • Upgrader from v1.X tiles to v2.0 channels

Describe alternatives you've considered
@saskiad additional details probably needed before someone tackles this

Additional context
Note, depends on #1173

https://alleninstitute.sharepoint.com/:w:/r/sites/NeuralDynamics/_layouts/15/Doc.aspx?sourcedoc=%7BE27B889D-27A1-4CC0-948C-10ADBE605654%7D&file=Data+Schema+2.0.docx&action=default&mobileredirect=true&DefaultItemOpen=1

@dbirman dbirman added the breaking Breaking changes label Dec 6, 2024
@saskiad
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saskiad commented Dec 7, 2024

Channel:

  • emission information needs to be more specific. current version is based on emission filters being in a wheel, so the wheel index tell us the emission wavelength, etc. I think that should be contained here
  • Channel is used for in vitro imaging (acquisition) but also in vivo (ophys) imaging, so need to make sure it works for both of those
  • Might need to be a base Channel class and then a few child classes. (e.g. the dilation only applies to slap, so it could be a slap channel thing).

Tile/Acquisition Tile:

  • Don't deprecate these, but remove the channel field from the acquisition tile

In acquisition:

  1. add a channels field that is a required list. This uses a Channel object that has the base channel info (above) plus a lit of acquisition tiles.
  2. Remove the tiles from acquisition class

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