CLI Reference#
placecell#
Placecell analysis pipeline.
Usage
placecell [OPTIONS] COMMAND [ARGS]...
analysis#
Run the place cell analysis pipeline.
Single dataset: placecell analysis -c config.yaml -d data.yaml Batch mode: placecell analysis -c config.yaml -d a.yaml -d b.yaml -y
Usage
placecell analysis [OPTIONS]
Options
- -c, --config <config>#
Required Analysis config file path or config ID.
- -d, --data <data_paths>#
Required Per-session data YAML file(s). Repeat for batch mode.
- -o, --output <output>#
Output bundle path or directory.
- -y, --yes#
Skip confirmation prompt and run full analysis.
- --show#
Open QC figures interactively before the confirmation prompt.
- -w, --workers <workers>#
Number of parallel worker processes for analyze_units.
- Default:
1
- --subset-units <subset_units>#
Keep only the first N neural units (for generating small test data).
- --subset-frames <subset_frames>#
Keep only the first N frames (for generating small test data).
- --force-redetect#
Force re-running detect-zones even when the cached zone_tracking CSV exists. Maze datasets only; ignored for arena.
define-zones#
Interactive zone definition tool (requires OpenCV).
Usage
placecell define-zones [OPTIONS]
Options
- -d, --data <data_path>#
Required Data config YAML (reads behavior_video and behavior_graph).
- --rooms <rooms>#
Required Number of rooms.
- --arms <arms>#
Required Number of arms.
detect-zones#
Run zone detection on tracking CSV using the zone graph.
Usage
placecell detect-zones [OPTIONS]
Options
- -d, --data <data_path>#
Required Data config YAML (reads behavior_position and behavior_graph).
- -o, --output <output>#
Output CSV path (default: zone_tracking_{stem}.csv).
- --interpolate <interpolate>#
Frame subsampling factor for video export (default: from config, or 5).
- --playback-speed <playback_speed>#
Playback speed multiplier for exported zone video (default: from config, or 10).