Problem on accessing OPHYS eye-tracking data

Technical
,
1

Hi everyone.
First of all I’m sorry for my poor English writing skill. I’ll try to convey my problem as clear as I can.
I’m currently working on ophys dataset and I’m using AllenSDK to access the data.
I wrote this piece of code to download only experiments that contains Eye tracking data.
here is my code:

experiments = boc.get_ophys_experiments(targeted_structures=[area]
                                            ,imaging_depths=depth
                                            ,session_types=['three_session_A']
                                            ,require_eye_tracking=True
                                            ,cell_specimen_ids=cells)
experiment_ids = [experiment[""id""] for experiment in experiments ]

Then i use these ids to get ophys experiments data and eye-tracking data using this code:

nwb = boc.get_ophys_experiment_data(ophys_experiment_id=experiments[0])

x = nwb.get_pupil_location()

but I got this error:

    849 except KeyError:
--> 850     raise NoEyeTrackingException("No eye tracking for this experiment.")
    852 return pupil_times, pupil_location

NoEyeTrackingException: No eye tracking for this experiment.

indeed I checked manually the metadata for this experiment (experiment id:652094901) using this code to ensure that eye-tracking data is available for this experiment. by this code:

>boc.get_ophys_experiments(ids = [652094901])
>[{'id': 652094901,
  'imaging_depth': 175,
  'targeted_structure': 'VISp',
  'cre_line': 'Slc17a7-IRES2-Cre',
  'reporter_line': 'Ai93(TITL-GCaMP6f)',
  'acquisition_age_days': 87,
  'experiment_container_id': 650389885,
  'session_type': 'three_session_A',
  'donor_name': '355468',
  'specimen_name': 'Slc17a7-IRES2-Cre;Camk2a-tTA;Ai93-355468',
  'fail_eye_tracking': False}]

as you can clearly see fail_eye_tracking key is false meaning that data is available.
but i did not stop and i found this method (part of brain_observatory_cache class) that returns an array with the shape of (n_frame,5) .
here is that method:
x = boc.get_eye_tracking(ophys_experiment_id=652094901)
in the doc string of this method i saw this comment:

        Returns
        -------
        `numpy.ndarray`
            Contents of array unknown. Assumed to be [n_frames, 5] where
            the meaning of the values in each column are unknown.
            Ask Saskia De Vries saskiad@alleninstitute.org

I’ve tried to email Saskia and to this day ive got no response.
finally I’ve ploted each column of this array and i found that first column must be time stamps:
image
but i have no idea about other columns.
Now my question is, is it even possible to get eye-tracking data using nwb.get_pupil_location() method or not? if not, what is the meaning of column that returned by boc.get_eye_tracking() method?
Thanks for your consideration and your time!

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2

Hi Mohammad,

I apologize that your email must have been buried while I was traveling.

The columns are:
frame number, eye_area, pupil_area, x_position, y_position.
The positions are both in degrees.

I think the get_pupil_location method doesn’t work for this data - I’m unclear why both functions exist and will ask the Technology team about that

Good luck!

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