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Adapt pipeline processing for cells with multiple autobias target voltages #535

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ru57y34nn opened this issue Oct 13, 2021 · 0 comments

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@ru57y34nn
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Describe the use case that is addressed by this feature.
This issue is related to Issue #533 and PR #534 which makes use of the autobias target voltage from the lab notebook. This issue specifically addresses instances where rig operators have either changed the autobias target voltage during the course of an experiment because they were unable to get stable recordings at the initial autobias target voltage level, or they have rerun certain stimulus sets at various autobias target voltages for scientific purposes. In either of these cases, we need to separate sweeps that have different autobias target voltages and only use sweeps that have the same autobias target voltage when extracting a set of features. This means, for example, that if a rig operator recorded the long_square sweeps (X3LP_Rheo) at multiple autobias target voltages, say at -60 and -80 mV, then we would want to extract two sets of long_square features, one set of long_square features for the -60 mV autobias target voltage and one set of long_square features for the -80 mV autobias target voltage level.

Describe the solution you'd like
Sweeps within a given NWB file need to be separated by autobias target voltage and separate sets of features need to be extracted at each autobias target voltage. This means that some cells will have multiple sets of the same features but collected at different voltages. This will likely require relatively major changes to the pipeline output jsons and to the features table in LIMS. Ideally LIMS would be able to handle multiple sets of features per cell, each set of features being at a different autobias target voltage. I am hoping that this issue will spark a conversation with the IPFX and LIMS teams so that we can determine the best way to accomplish this goal.

Describe alternatives you've considered
I am not aware of any alternative solutions for this issue.

Additional context
I have dug up several experiments that contain stimulus sets repeated at various autobias target voltages and extracted the sweeps numbers that were ran at each autobias target voltage for each stimulus set and saved them out as json files for reference. The json files are located here: //allen/programs/celltypes/workgroups/279/Rusty/multiple_autobias_v_jsons/

Do you want to work on this issue?
I can start working on a method to sort sweeps by autobias target voltage and modify the feature extraction output jsons to handle repeated features at various voltages but there will need to be some conversation about how to best get the repeated sets of features into LIMS.

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