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Mesoscope Saturation Threshold update #361

Closed samiamseid closed 10 months ago

samiamseid commented 10 months ago

Metric / Plot Impacted Physio pixel saturation

Update Motivation Pixel saturation on mesoscope isnt something we have had to worry about historically, as we have not had bright enough cre lines or powerful enough lasers to encounter saturated pixels. However, now we are running GCaMP8 mice and have an Axon laser, pixel saturation is a real possibility. The existing metric was an estimated value, and not accurate to the true saturation metric.

Requested Feature/Solution Change pixel saturation threshold to "18500"

Please provide the following information as appropriate:

Screenshots or example plots truesaturation Above screenshot shows the pixel saturation occurring on meso1

Scope Mesoscopes

samiamseid commented 10 months ago

Update: upon inspecting the data further, the actual saturation point is exactly 18423

seanmcculloch commented 10 months ago 
def get_dynamic_range(self):
    """Get the dynamic range for a particular scope.

    Returns: 
        An array corresponding to the min and max pixel value

    Raises: 
        NotImplementedError: For rigs where the dynamic range is not known.
    """
    if self.ophys_experiment is not None:
        rig = self.ophys_experiment.data_pointer['rig']
    else:
        return [0, 65535] # Default of 16-bit unsigned
        # TODO: Maybe calculate this?

    if rig in rigs.NIKON:
        px_range = [0, 4095] # 12-bit unsigned dynamic range
    elif rig in rigs.SCIENTIFICA:
        # 20181010 - new algorithm sub-pixel correction influencing metric, decreases dynamic range
        px_range = [0, 65533] # 16-bit unsigned dynamic range
    elif rig in rigs.DEEPSCOPE:
        px_range = [0, 2**14]
    elif rig in rigs.MESOSCOPE:
        px_range = [0, 22500] # From Natalia 20180622
    else:
        raise NotImplementedError('Dynamic range is not known for rig {}'.format(rig))
    return px_range
macarenasa commented 10 months ago

Action items/next meeting