Configuration Schema

Full reference for ~/.optari/config/config.json. All fields are required unless noted, and every edit needs an app restart.

general

Field	Type	GUI	Meaning
LOG_LEVEL	string	Settings ▸ General	Terminal log verbosity (e.g. "INFO" / "WARNING").
GUI_LOG_LEVEL	string	Settings ▸ General	Verbosity of messages surfaced as in-app napari notifications (e.g. "INFO" / "WARNING").
DEFAULT_PA_LAYER	string	Settings ▸ Viewer	Name of the OA reconstruction layer selected by default when a scan loads.
PA_FALLBACK_SCALE	[frame, z, x]	Settings ▸ Viewer	Fallback mm/pixel scale for OA layers when FOV metadata is missing.
DEFAULT_US_LAYER	string	hidden	Name of the default US layer (not implemented, no effect).
US_FALLBACK_SCALE	[frame, z, x]	Settings ▸ Viewer	Fallback mm/pixel scale for US layers.
DEFAULT_FRAME_INDEX	int, "spectral_motion", "frame_motion", "acquisition_start" or "roi"	Settings ▸ Viewer	Fixed starting frame index, "spectral_motion" or "frame_motion" for the frame with the least motion of that kind (see Automatic Frame Selection), "acquisition_start" for the frame where recording started (ithera scans), or "roi" for the first frame holding one of the scan's stored ROIs (0 if it has none).
DEFAULT_CHANNEL_INDEX	int	Settings ▸ Viewer	Default acquisition channel (as integer index).
DEFAULT_PLAYBACK_FPS	int	Settings ▸ Viewer	Frame playback speed.
OPERATOR	string	Settings ▸ General	Who is running the analysis. Will be recorded in the exported HDF5 and Excel files.
ANALYSIS_ID	string	Settings ▸ General	Name of the analysis, e.g. a study or cohort name. Will be recorded in the exported HDF5 and Excel files.
LAYER_COLOR_MAPS	object	Settings ▸ Viewer	Colormap per layer type, e.g. {"ultrasounds": "gray", "reconstructions": "viridis", "unmixed": "magma", "so2": "twilight_shifted", "thb": "inferno"}.
DEFAULT_VISIBLE_DOCKS	object of label → 0/1	Settings ▸ Docks	Which panels are visible when OPTARI starts (see OPTARI ▸ Docks). A missing label defaults to visible. Applies on every launch, overriding napari's own remembered window layout.

annotation

Field	Type	GUI	Meaning
roi_colors	list of hex strings	Settings ▸ ROI Table	Color palette cycled through for ROI shape colors in the viewer.
roi_features	object of name → 0/1	Settings ▸ ROI Table	Which ROI features are shown in the Live Analysis table (The saved/exported data always includes the full feature set regardless of this setting, see ROI Annotation.
show_track_id	bool	Settings ▸ Viewer	Label ROI shapes as roi_id/track_id instead of just roi_id.
roi_label_size	int	Settings ▸ Viewer	Text size of the ROI shape labels in the viewer.

Available feature names:

roi_id, track_id, roi_group_uid, mean, median, std, p10, p90, iqr, min, max, snr, n_pixels, size_mm, intensity_filter, filter_min, filter_max, src_layer, kind, roi_source, study_folder, scan_folder, scan_name, frame, channel, roi_ts, scan_ts, roi_centroid, roi_geometry, filepath.

A fixed set of columns (roi_id, track_id, roi_group_uid, study_folder, scan_folder, scan_name, frame, channel, src_layer, roi_ts, kind, scan_ts, filepath) is always included in the Saved Analysis table, independent of the live-visibility settings here, so saved records are always fully identifiable.

OPTARI identifies an ROI at three scopes. roi_id is one shape on one frame, a per-session counter, and it is the number drawn on the shape in the viewer. track_id links the copies of one ROI across frames within a session. roi_group_uid is the group's unique identity.

src_layer names the image layer an ROI was measured on, and roi_source who drew the ROI: OPTARI, or the iLabs file it came from (iAnnotation, iROIList). roi_geometry is a JSON dictionary holding the ROI vertices in PATATO coordinates (metres, origin at the image centre) together with its shape kind, tissue class and source. It uses the same field of view-independent representation as ROI presets and the HDF5 ROI export, so a saved ROI should stay anatomically correct if it is later restored onto a reconstruction with a different FOV. It is exported by default but hidden from the tables unless enabled here.

analysis

Field	Type	GUI	Meaning
histogram_bins	int	Settings ▸ General	Bin count for the Histogram plot.

segmentation

Field	Type	GUI	Meaning
default_model	string	Settings ▸ Models	Model id (from segmentation_models.json) selected by default. See Segmentation Models.

Schema versioning

config.json contains a schema_version field. If OPTARI detects that your existing configuration was written by an incompatible older version, it automatically:

1. Renames your existing ~/.optari/config folder to a timestamped backup, ~/.optari/config_old_<timestamp>.
2. Creates a fresh ~/.optari/config from the packaged defaults, including the default presets.
3. Your previous settings and all your presets (including your own ROI, batch, segmentation, reconstruction and unmixing presets) are kept in the backup folder and can be modified and copied back.