Saved Data and Video

The Training Village automatically handles all aspects of data collection, including raw and processed behavioral datasets, video recordings, video-tracking coordinates, and system metrics.

Directory Hierarchy & Folder Structure

The village_projects/ directory is structured as follows:

village_projects/
└── projectName/
    ├── code/
    ├── media/
    └── data/

A dedicated folder is created for each project using the specified project name. Each project contains three subdirectories:

  • code/: Stores all executable Python source code and experiment-specific scripts. See the PROTOCOL & TASK DESIGN section for a detailed breakdown.

  • media/: (Optional) Stores audio tracks, videos, or image assets required by behavioral tasks.

  • data/: Central repository for all experimental outputs, including raw and processed data files and videos.

Inside the Data Folder

data/
├── sessions/
├── videos/
└── systemName/

  • sessions/: Contains one subfolder per animal with raw and parsed session datasets.

  • videos/: Contains one subfolder per animal with video recordings.

  • systemName/: Named after your system ID; contains platform-wide metrics and hardware logs.

System Configuration Folder (systemName/)

systemName/
├── rsync_logs/
├── data_removal_logs/
├── old_events/
├── events.csv
├── subjects.csv
├── sessions_summary.csv
├── bpod_water_calibration.csv
├── sound_calibration.csv
├── temperatures.csv
└── deleted_sessions.csv

Core Data Files

  • events.csv: Log of all system events. Columns: date, type, subject, description.

  • subjects.csv: Table with one row per subject, used to track the settings that will be applied in each subject’s next session. Columns: name, tag, basal_weight, active, next_session_time, next_settings. The next_settings field is a JSON string containing the parameters computed for the upcoming session, including next_task and refractory_period. The next_session_time field indicates the earliest time at which the subject is eligible for another session; it is calculated by adding refractory_period to the end time of the previous session.

  • sessions_summary.csv: Summary table of all completed sessions. A new row is appended each time a session ends. Columns: date, subject, tag, weight, task, duration, trials, water, settings.

    Note

    For the water column to be populated, water intake must be explicitly recorded within the task definition (see PROTOCOL & TASK DESIGN).

Other Data Files

  • temperatures.csv: Hourly temperature and humidity log, recorded automatically. Columns: date, temperature, humidity.

  • calibration_files.csv: Registry of saved calibration files. Different calibration types can be created and customized (e.g. sound_calibration, camera_calibration, bpod_water_calibration), and their stored values can be retrieved and used within tasks.

  • deleted_sessions.csv: List of manually deleted sessions.

    Important

    Deleting a session never removes the underlying data — it simply adds an entry to this list, causing the session to be excluded from sessions_summary.csv and from the per-subject global session file.

Log Folders

  • rsync_logs/: Log of every data synchronization and backup attempt with a remote server or external drive, regardless of whether it succeeded or failed.

  • data_removal_logs/: Log of the deletion process for videos that have already been synchronized to a remote server or external drive.

  • old_events/: To prevent events.csv from growing too large, a new file is created once a line threshold is exceeded. Older event records are archived here.

Video Recordings & Frame Data

  • Storage path: data/videos/{subject}/

  • Filename format: {subject}_{task}_{timestamp}

Each recording session produces two files:

  • {filename}.mp4: H.264-encoded video. Default resolution is 640×480 at 30 FPS (configurable via system settings).

  • {filename}.csv: Per-frame data table:

Column

Description

frame

Frame index.

trial

Active trial number during that frame.

annotation

Custom text string pushed dynamically from the running protocol.

timestamp

Absolute hardware sensor capture time.

x_position

Center-of-mass X coordinate of the animal (tracking must be enabled).

y_position

Center-of-mass Y coordinate of the animal (tracking must be enabled).

Frame Annotations & On-Screen Overlays

Both cameras render diagnostic text overlays burnt directly into the video frames.

Operant box camera:

  • Top row: <filename>  trial: N  <annotation text> — filename, trial number, and optional custom text set from within the task.

  • Bottom row: <duration>  frame: N  area1: N  area2: N... — elapsed recording time, frame number, and pixel counts for each active tracking area.

Corridor camera:

  • Top row: <filename>  <annotation text> — filename and the timestamp and description of the most recent system event (no trial number, as the corridor is not trial-structured).

  • Bottom row: <duration>  frame: N  area1: N  area2: N... — same format as above.

In addition to the text overlays, when VIEW_DETECTION is enabled the system burns two additional visual layers directly into the saved video: the detection pixels highlighted in black, and the boundary lines delimiting each active tracking area. This option is configurable under MONITOR → DETECTION SETTINGS. For performance reasons, these overlays are computed on the same stream used for the live display and the saved recording.

Tip

We recommend keeping VIEW_DETECTION_CORRIDOR permanently enabled for the corridor camera. Corridor recordings are not critical data, but having the overlay active makes it easy to verify at a glance that pixel detection is working correctly across all areas.

For the operant box, we recommend keeping VIEW_DETECTION_BOX disabled during normal operation so that task videos are saved clean. Because the operant box is typically a closed, controlled environment, illumination conditions are stable and threshold recalibration is rarely needed. When it is required, simply enable VIEW_DETECTION_BOX, adjust the thresholds, and disable it again.

Subject Behavioral Sessions

  • Storage path: data/sessions/{subject}/

  • Filename format: {subject}_{task}_{timestamp}

Three files are generated for every completed behavioral session:

data/sessions/{subject}/
├── {filename}_RAW.csv
├── {filename}.csv
└── {filename}.json

1. Raw Session ({filename}_RAW.csv)

Created in real time, one row per event:

Column

Description

TRIAL

Trial index.

START

Absolute Unix timestamp (4 decimal places) marking the onset of a state or event.

END

Absolute Unix timestamp of state termination (empty for instantaneous events).

MSG

Message type (see standards below).

VALUE

Value associated with the message.

Message type standards (MSG):

  • _Transition_to_{stateName}: State machine transition flag.

  • STATE_{stateName}_START / STATE_{stateName}_END: Structural boundaries of a behavioral state.

  • Hardware event name: Digital input/output line transitions (e.g., photo-gate beams, ports).

  • Custom variable tag: Any performance variable explicitly captured with register_value() (e.g., stimulus_side, correct_choice, rewarded). The tag name is written to MSG and its value to VALUE.

  • TRIAL_START / TRIAL_END: Absolute trial boundary markers.

2. Processed Session ({filename}.csv)

A parsed, trial-by-trial overview generated at the end of each trial by processing the raw data. Instead of one row per event, this file contains one row per trial. It begins with the following fixed columns: session, date, trial, subject, task, system_name, run_mode.

run_mode

The run_mode field is set to manual if the session was launched manually from the GUI, or auto if it was triggered automatically upon detecting an animal in the corridor.

3. Session Settings Metadata ({filename}.json)

Stores all parameters used during the session: minimum_duration, maximum_duration, run_mode, observations, and all custom protocol parameters.

To add a note to a session, click on its entry in sessions_summary within the GUI. A panel listing all session parameters will appear; the observations field is editable and empty by default.

Tip

Although .json files already capture all parameters used in a session, it is good practice to also record relevant variables from within the task using register_value(), as this makes them directly accessible in the .csv file.

Aggregate History File

In addition to the per-session files, a persistent history file is maintained in each subject’s directory:

  • {subject}.csv: Compiles every historical session completed by that animal. New session rows are appended each time a session ends. This aggregate dataset is essential for adaptive automated training (training_protocol.py), allowing the system to evaluate progression milestones — for example, verifying whether an animal achieved >80% accuracy over its last three sessions before advancing to the next training stage.

Understanding the Automated Training Loop

The Training Village uses a closed-loop parameter cycle to drive fully autonomous training progression across days without requiring human intervention:

              [ subjects.csv ]
         (Reads current next_settings)
                     │
                     ▼
        [ Active Behavioral Session ]
                     │
       (Saves parameters actually used)
                     ▼
             [ {filename}.json ]
                     │
       (Session ends → training_protocol.py
        evaluates performance history)
                     ▼
  [ Updated next_settings in subjects.csv ]

  1. Initialization: When an animal is recognized, its profile variables are loaded from the next_settings field in subjects.csv.

  2. Archiving: The parameters used for the current session are saved to {filename}.json.

  3. Evaluation: At the end of the session, training_protocol.py runs automatically and analyzes the animal’s historical performance trends from {subject}.csv.

  4. Update: The script computes the adjusted parameters for the next session (advancing stages, modifying task variables, or updating the refractory period) and writes them back to the next_settings field in subjects.csv.