Raw Data Structure

What does the raw data look like just after acquisition?

./
└── 2022-02-24_9-57-53_mouse-0898
    ├── 2022-02-24_09-57-55_mouse-0898
    │   ├── 103_ADC1.continuous
    │   ├── 103_ADC2.continuous
    │   ├── 103_ADC3.continuous
    │   ├── 103_ADC4.continuous
    │   ├── 103_ADC5.continuous
    │   ├── 103_ADC6.continuous
    │   ├── 103_ADC7.continuous
    │   ├── 103_ADC8.continuous
    │   ├── 103_AUX1.continuous
    │   ├── 103_AUX2.continuous
    │   ├── 103_AUX3.continuous
    │   ├── Continuous_Data.openephys
    │   ├── all_channels.events
    │   ├── messages.events
    │   ├── notebook.mat
    │   ├── settings.xml
    │   └── stimlog.txt
    ├── Laser_mouse-0898_2022-02-24T09_57_53.csv
    ├── Sky_mouse-0898_2022-02-24T09_57_53.csv
    ├── Sky_mouse-0898_2022-02-24T09_57_53.mp4
    └── TTL_mouse-0898_2022-02-24T09_57_53.csv

Timestamps

All have two columns, one row for each frame. The first is some data, the second an isoformatted timestamp

• Laser_mouse-{mouse_id}_{timestamp}.csv - laser on/off (bool) for each frame

• Sky_mouse-{mouse_id}_{timestamp}.csv - samples since camera on (unused)

• TTL_mouse-{mouse_id}_{timestamp}.csv - TTL pulse on/off (bool) for each frame

Video

• Sky_mouse-{mouse_id}_{timestamp}.mp4 - Top-down view of arena

Open Ephys

Within a folder with name {timestamp}_mouse-{mouse_id}

Todo

Document which continuous files are which value

• .continuous files - raw timeseries of accelerometers and laser pulses

• stimlog.txt - .txt (actually .json) version of stimlog within notebook.mat

• notebook.mat - Experimental conditions for each trial

  • Example notebook file containing nb and stimlog

  nb =
  
  struct with fields:
  
             user: 'Molly'
          mouseID: '0894'
            Depth: 'unknown'
         datapath: 'Z:\lab\djmaus\Data\Molly'
        activedir: '\\wehrrig4\d\lab\djmaus\Data\Molly\2022-02-24_11-24-42_mouse-0894\2022-02-24_11-24-44_mouse-0894'
       LaserPower: 'unknown'
         mouseDOB: 'unknown'
         mouseSex: 'm'
    mouseGenotype: 'vgat-chr2'
            Drugs: 'none'
            notes: [5×10 char]
    Reinforcement: 'none'
  

  >> stimlog(1)
  
  ans =
  
  struct with fields:
  
                    type: 'silentsound'
                   param: [1×1 struct]
           protocol_name: 'SingleLaserFlag'
    stimulus_description: 'silentsound loop_flg:0 duration:100 ramp:0 next:1000'
    protocol_description: 'single laser ON flag for front-panel controlled laser stim'
        PlottingFunction: 'none'
                 version: 'djmaus'
               timestamp: 'February-24-2022 11:24:45.157'
              LaserOnOff: 1
              LaserStart: 0
              LaserWidth: 10
          LaserNumPulses: 4800
                LaserISI: 10