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incorrect values for imaging_depth column in VisualBehaviorOphysProjectCache ophys_experiment_table #2745

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matchings opened this issue Aug 3, 2024 · 2 comments
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@matchings
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There are two columns related to the imaging depth for 2-photon imaging experiments, one is targeted_imaging_depth which should be the intended depth for the experiment, and the other is imaging_depth which is the actual depth recorded by the 2-photon microscope after zeroing on the cortical surface (which can be slightly variable day to day) and moving to the intended field of view based on the best match to previous recording days with the same field of view.

The targeted_imaging_depth should be the same for all sessions recorded from the same field of view (indicated by its ophys_container_id). The imaging_depth will inevitably differ slightly from day to day.

In the current version of AllenSDK (2.16.2) and visual behavior ophys dataset (v1.1.0), the values for these two columns are identical, which is clearly a mistake.

image

Given that the values are always intervals of 5, i believe that both values represent the targeted_imaging_depth (i.e. the imaging_depth column is incorrect).

I am not sure where this error was introduced, but it should either be fixed (the preferred option), or the documentation in the code (and all other relevant locations) should be updated to reflect the fact that these columns are the same and both represent the intended target depth, not the actual measured value.

@matchings matchings added the bug label Aug 3, 2024
@matchings
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Tagging @morriscb as i believe he may have implemented the update that added the targeted_imaging_depth column in fall of 2023 during the final release of the VBO dataset

@matchings
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I'll also note that the changelog in the readthedocs page says that the targeted_imaging_depth was intended to be the average depth across the container, which would result in values other than those in increments of 5um, which makes me think that neither of these columns are providing what they intend to provide.

image

readthedocs page: https://allensdk.readthedocs.io/en/latest/visual_behavior_optical_physiology.html

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