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Support for data tracked in Bonsai #348

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sfmig opened this issue Nov 22, 2024 · 1 comment
Open

Support for data tracked in Bonsai #348

sfmig opened this issue Nov 22, 2024 · 1 comment
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enhancement New optional feature

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@sfmig
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sfmig commented Nov 22, 2024

It would mean adding a loader function to load points (centroid of a blob?) tracked by Bonsai.

We would need:

  • an example file (we have one from Dario but we don't know if it is standard)

Questions:

  • in Bonsai, is there a standard format to export data or do users define the header of the csv? (@lochhh may know this already)
  • if there is a standard, does it change between Bonsai versions?

See also #308

@roaldarbol
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roaldarbol commented Nov 22, 2024

I've got a Bonsai reader in animovement, the code is here: https://github.com/roaldarbol/animovement/blob/main/R/read_bonsai.R

And the sample data - would be good to compare and see if they follow the same format (the relevant columns contain Centroid): https://github.com/roaldarbol/animovement/blob/main/tests/data/bonsai/LI850.csv

Bonsai also allows multiple ROIs which I'm not supporting yet (the data above has 6 ROIs if I remember correctly); the data structure really seems to depend on the workflow. I'm sure it can be dealt with with some regex, but I haven't attempted yet.

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Labels
enhancement New optional feature
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