Configuration Reference

Complete reference for all configuration options in config.ini.

File Structure

[configsection]
config = section_name

[section_name]
# Camera settings
# Processing settings
# Trial settings
# Reward settings

CLNF Configuration Sections

raspicambrain_reward_punish_1roi

Single ROI configuration for CLNF experiments.

[raspicambrain_reward_punish_1roi]
vid_source = PiCameraStream
data_root = /media/pi/data/cl_brain/
raw_image_file = image_stream.hdf5
resolution = 256, 256
framerate = 15
awb_mode = off
shutter_speed = 60000
iso = 800
sensor_mode = 7
dff_history = 6
ppmm = 25.6
bregma = 135, 128
seeds_mm = {"ALM": {"ML": 1.5, "AP": 2.5}, ...}
roi = M1_L
roi_size = 0.3, 0.3
audio = 1
n_tones = 18
audio_delay = 0
reward_delay = 1
reward_threshold = 0.075
adaptive_threshold = 1
total_trials = 60
max_trial_dur = 30
success_rest_dur = 10
fail_rest_dur = 15
initial_rest_dur = 30
summary_file = expt_1roi_trial_summary.csv
summary_header = mouse_id, session, data_path, start, end, duration, fps, dff_history, n_tones, reward_threshold, rewards, audio, session_type

raspicambrain_reward_punish_2roi

Dual ROI configuration for CLNF experiments.

[raspicambrain_reward_punish_2roi]
vid_source = PiCameraStream
data_root = /media/pi/data/cl_brain/
raw_image_file = image_stream.hdf5
resolution = 256, 256
framerate = 15
awb_mode = off
shutter_speed = 60000
iso = 800
sensor_mode = 7
dff_history = 6
ppmm = 25.6
bregma = 135, 128
seeds_mm = {"ALM": {"ML": 1.5, "AP": 2.5}, ...}
roi_operation = BC_L-BC_R
roi_size = 0.3, 0.3
audio = 1
n_tones = 18
audio_delay = 0
reward_delay = 1
reward_threshold = 0.1
adaptive_threshold = 0
total_trials = 60
max_trial_dur = 30
success_rest_dur = 5
fail_rest_dur = 10
initial_rest_dur = 30
summary_file = expt_2roi_trial_summary.csv
summary_header = mouse_id, session, data_path, start, end, duration, fps, dff_history, n_tones, reward_threshold, rewards, audio, session_type

CLMF Configuration Sections

sentech_dlclive

Configuration for CLMF experiments with DeepLabCut-Live.

[sentech_dlclive]
vid_source = SentechCameraStream
data_root = /media/murphy/fast_storage/data/
video_file = behavior_video.mp4
resolution = 640, 320
framerate = 30
awb_mode = off
shutter_speed = 60000
iso = 800
joint_history_sec = 5
ppmm = 3.5
bregma = 108, 128
control_point = fl_l
start_center = 590,110
start_radius_mm = 4
target_center = 590,80
target_radius_mm = 6
speed_threshold = 20
audio = 1
n_tones = 18
audio_delay = 0
reward_delay = 1
reward_threshold_mm = 5
adaptive_threshold = 0
total_trials = 10
max_trial_dur = 30
success_rest_dur = 10
fail_rest_dur = 10
initial_rest_dur = 30
dlc_model_path = /path/to/dlc-model/
summary_file = expt_dlclive_summary.csv
summary_header = mouse_id, session, data_path, start, end, duration, fps, n_tones, start_radius, target_radius, rewards, audio, session_type

Parameter Descriptions

Camera Settings

Parameter Description Example
vid_source Camera driver class PiCameraStream, SentechCameraStream
resolution Image width, height 256, 256 or 640, 320
framerate Frames per second 15, 30, 60
awb_mode Auto white balance off, auto
shutter_speed Camera shutter speed (μs) 60000, 600000
iso Camera ISO 800
sensor_mode PiCamera sensor mode 7

Processing Settings

Parameter Description Example
dff_history Frames for baseline calculation 6
ppmm Pixels per millimeter 25.6, 3.5
bregma Bregma landmark (row, col) 135, 128
seeds_mm Brain region coordinates (JSON) {"ALM": {"ML": 1.5, "AP": 2.5}}

ROI Settings

Parameter Description Example
roi Single ROI name M1_L
roi_operation Dual ROI operation BC_L-BC_R, M1_L+ALM
roi_size ROI size in mm 0.3, 0.3
start_center Start ROI center (pixels) 590, 110
start_radius_mm Start ROI radius (mm) 4
target_center Target ROI center (pixels) 590, 80
target_radius_mm Target ROI radius (mm) 6

Audio Settings

Parameter Description Example
audio Enable audio feedback 0 or 1
n_tones Number of frequency bins 18
audio_delay Audio delay (frames) 0

Reward Settings

Parameter Description Example
reward_threshold ΔF/F threshold (CLNF) 0.075
reward_threshold_mm Distance threshold (CLMF) 5
speed_threshold Speed threshold (CLMF) 20
reward_delay Reward delay (frames) 1
adaptive_threshold Enable adaptive threshold 0 or 1

Trial Settings

Parameter Description Example
total_trials Number of trials 60
max_trial_dur Max trial duration (sec) 30
success_rest_dur Rest after success (sec) 10
fail_rest_dur Rest after failure (sec) 15
initial_rest_dur Initial rest period (sec) 30

DeepLabCut Settings (CLMF)

Parameter Description Example
dlc_model_path Path to DLC model /path/to/model/
control_point Body part to track fl_l
joint_history_sec Stability history (sec) 5

Data Output Settings

Parameter Description Example
data_root Base data directory /media/pi/data/
raw_image_file HDF5 file name image_stream.hdf5
video_file Video file name behavior_video.mp4
summary_file Summary CSV name expt_summary.csv
summary_header CSV column names (comma-separated)

Brain Region Coordinates

Default seed positions (in mm from bregma):

Region ML AP
ALM 1.5 2.5
M1 1.86 0.64
M2 0.87 1.42
FL 2.45 -0.57
HL 1.69 -1.15
BC 3.46 -1.73
V1 2.52 -3.77
RS 0.62 -2.89

Editing Configuration

  1. Open config.ini in a text editor
  2. Find the appropriate section
  3. Modify values as needed
  4. Save the file

ROI Position Adjustment

After running the preview, ROI positions are saved back to config.ini. You can also manually specify coordinates:

m1_l = 76,114,8,8

Format: x, y, width, height