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Interface for experimental protocols

GUI

The interface is minimal:

  1. Pick the modality that you want to have by checking the upper boxes.

    N.B. the Camera initialization might take 5-6 seconds after clicking

  2. Pick the configuration that you want to use.

    The set of configuration is loaded from the files in the protocols/ folder.

    Each file should be a JSON file, it specifies some key metadata related to the experiment:

    {
 "NIdaq-acquisition-frequency":1000,
 "NIdaq-analog-input-channels":1,
 "NIdaq-digital-input-channels":2,
 "Screen":"Dell-P2018H",
 "FaceCamera-frame-rate":10,
 "STEP_FOR_CA_IMAGING_TRIGGER":{"channel":0,
 			   "onset": 0.1,
 			   "duration":0.3,
 			   "value":5.0},
 "root_datafolder":"DATA",
 "subjects_file":"mice_yann.json",
 "experimenter":"Yann Zerlaut",
 "lab":"Rebola and Bacci labs",
 "institution":"Institut du Cerveau et de la Moelle, Paris",
 "protocols":"all" # can be a subset of protocols: ["Pakan-et-al-Elife-2016","sparse-noise-30-min-large-square"]
 }

  3. You need to pick the subject.

    In a given configuration, you specify a "subjects_file". You can then choose which subject from the entries of the file.

    This subject file is also a JSON file with a set of entries specified as follows:

    {
 "Mouse1_WT":{"description":"Mouse1_WT",
 	 "anibio":"1513487",
 	 "sex":"Male",
 	 "strain":"C57B6/J",
 	 "genotype":"Wild-Type",
 	 "species":"Mouse",
 	 "subject_id":"Mouse1",
 	 "weight":"",
 	 "virus":"GCamp6f",
 	 "surgery":"",
 	 "aka":"George Benson",
 	 "date_of_birth":"2020_12_07"},
 "Mouse2_WT":{"description":"Mouse2_WT",
 	 "anibio":"1513487",
 	 "sex":"Male",
 	 "strain":"C57B6/J",
 	 "genotype":"Wild-Type",
 	 "species":"Mouse",
 	 "subject_id":"Mouse2",
 	 "weight":"",
 	 "virus":"GCamp6f",
 	 "surgery":"",
 	 "aka":"Wes Montgomery",
 	 "date_of_birth":"2020_12_07"}
 	 }

    You can add any additional key to this. They will appear in the subject metadata of the datafile.

  4. Load a visual stimulation protocol

    Either None or one of the protocols stored in the protocols/ folder (and, if "protocols" is not set to "all", specified in the configuration file).

  5. Click "Init", wait 1-2s, and click "Run" to launch the recording.

Under the hood

Using separate threads for the different processes using the multiprocessing module, we interact with those threads by sending "record"/"stop" signals. The different threads are:

  • The NIdaq recording

  • THe visual stimulation

  • The FLIR-camera

Full install for experimental setups

pip install psychopy
pip install nidaqmx