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AllenInstitute / brain_observatory_qc

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Information on expected frame rates is needed #143

Open DowntonCrabby opened 1 year ago

DowntonCrabby commented 1 year ago

Description of needed information Information on expected frame rates is needed for the physio datastream. The expected frame rate is determined by several factors including microscope type, number of planes being imaged, resolution of each field of view etc.

We need a way to parse this metadata and create calculations that will give us what we expect the frame rate to be for all types of imaging sessions that will be qced on the mouse-seeks platform.

Once the expected frame rate is calculated and determined we will need scientific and/or operations leads to set qc tolerance thresholds (i.e. how much wiggle room is acceptable is the frame rate is not quite as it should be).

matchings commented 1 year ago

@DowntonCrabby I just re-assigned this to Natalia and Sam because I think they are much more knowledgeable about how to parse the data coming off the rig to gather this information than either Pete and I are

nataliaorlova commented 1 year ago

For Mesoscope multi-plane imaging, the logic finding out the pair-wise frame rate should be total frame rate divided by a number of pairs in the session. The total frame rate can be found in the dictionary that Mesoscope splitter module saves in {exp_id}.h5 field 'scanimage_metadata' under the key 'SI.hRoiManager.scanFrameRate'.

matchings commented 9 months ago

@seanmcculloch @DowntonCrabby this seems like something useful to add to mouse QC, if it hasnt been already