API Reference

BioImageViewer

from anybioimage import BioImageViewer
viewer = BioImageViewer()

Method	Description
`set_image(data)`	Load a numpy array or `BioImage` object
`set_plate(path)`	Load an OME-Zarr HCS plate

Method	Description
`add_mask(labels, name, color, opacity, visible, contours_only, contour_width)`	Add a mask layer; returns `mask_id`
`set_mask(labels, ...)`	Replace all masks with a single mask
`remove_mask(mask_id)`	Remove a mask by ID
`clear_masks()`	Remove all masks
`update_mask_settings(mask_id, **kwargs)`	Update mask properties
`get_mask_ids()`	List all active mask IDs

Method	Description
`enable_sam(model_type)`	Enable SAM segmentation
`disable_sam()`	Disable SAM

Property	Type	Description
`image_visible`	`bool`	Toggle image layer
`image_brightness`	`float`	Brightness adjustment (−1 to 1)
`image_contrast`	`float`	Contrast adjustment (−1 to 1)
`dim_t`	`int`	Number of time points (read-only)
`dim_c`	`int`	Number of channels (read-only)
`dim_z`	`int`	Number of Z slices (read-only)
`current_t`	`int`	Current time index
`current_z`	`int`	Current Z index
`_channel_settings`	`list[dict]`	Per-channel name, color, min, max, visible
`canvas_height`	`int`	Widget canvas height in pixels (default 800)
`use_jpeg_tiles`	`bool`	Use JPEG tile encoding for smaller payloads (default `False`; useful on remote JupyterHub)
`scenes`	`list[str]`	Available scenes for multi-scene files (read-only)
`current_scene`	`str`	Active scene name

Property	Type	Description
`rois_df`	`DataFrame`	Rectangles: id, x, y, width, height
`polygons_df`	`DataFrame`	Polygons: id, points, num_vertices
`points_df`	`DataFrame`	Points: id, x, y
`masks_df`	`DataFrame`	Masks: id, name, visible, opacity, color
`tool_mode`	`str`	Active tool: `pan`, `select`, `draw`, `polygon`, `point`
`roi_color`	`str`	Rectangle color (hex)
`polygon_color`	`str`	Polygon color (hex)
`point_color`	`str`	Point color (hex)
`point_radius`	`int`	Point radius in pixels
`rois_visible`	`bool`	Toggle rectangle visibility
`polygons_visible`	`bool`	Toggle polygon visibility
`points_visible`	`bool`	Toggle point visibility