Quick Start Guide¶

Get up and running with CLoPy in minutes.

Running Your First Experiment¶

CLNF Experiment (Single ROI)¶

cd clopy
python brain/cla_reward_punish_1roi.py

CLNF Experiment (Dual ROI)¶

cd clopy
python brain/cla_reward_punish_2roi.py

CLMF Experiment¶

cd clopy
python behavior/cla_dlc_trials_speed.py

What Happens Next¶

Mouse ID Prompt: Enter your mouse identifier Please enter mouse ID: M001
Preview Window: A preview window appears showing:
- Live camera feed
- ROI positions (draggable rectangles)
- DFF (ΔF/F) visualization
- Luminosity sparklines
Verify Setup: Ensure:
- Camera is properly positioned
- ROI covers the target brain region
- Bregma landmark is visible
- Lighting is adequate
Start Session: Press Esc to begin the experiment
During Experiment:
- Trials start automatically after initial rest period
- Audio tones play during active trials
- Green LED flashes on successful trials
- Red LED flashes on failed trials
End Session: Press Esc to stop early, or let it complete

Understanding the Trial Flow¶

┌─────────────────────────────────────────────────────────────┐
│                      Trial Structure                        │
├─────────────────────────────────────────────────────────────┤
│                                                             │
│  ┌──────────┐    ┌──────────────┐     ┌────────────┐        │
│  │  Rest    │───▶│    Trial     │───▶│  Outcome   │        │
│  │ Period   │    │   (max 30s)  │     │            │        │
│  └──────────┘    └──────────────┘     └────────────┘        │
│  10-15 seconds                             │                │
│                                            ▼                │
│                                    ┌───────┴───────┐        │
│                                    │               │        │
│                                Success            Fail      │
│                                (reward)         (buzzer)    │
│                                   │                │        │
│                                   ▼                ▼        │
│                                10s rest        15s rest     │
│                                                             │
└─────────────────────────────────────────────────────────────┘

Key Controls¶

Key	Action
`Esc`	Start/Stop experiment
Mouse Drag	Move ROI positions
`Esc` (during trial)	Abort session

Data Output¶

After each session, data is saved to:

data_root/mouse_id/YYYYMMDDHHMMSS/
├── config.ini              # Session configuration
├── image_stream.hdf5       # Raw imaging data (CLNF)
├── video.mp4               # Behavior video (CLMF)
└── VideoTimestamp.txt      # Trial-by-trial log

Configuration First¶

Before running experiments, you'll need to configure:

Camera settings in config.ini
ROI positions (brain regions)
Reward thresholds
Trial parameters

See Configuration Guide for details.