scallops.visualize.imshow.plot_plate

scallops.visualize.imshow.plot_plate(exp, plate_shape=(8, 12), well_shape=(5, 5), channel=0, time=0, zaxis=0, well_layout=9, vmax='', vmin='', full_well=None, max_workers=-1, **kwargs)

Plot raw images per channel in the whole plate layout (mimics heatmap plot).

Parameters:

  • exp (Experiment) – Experiment instance.

  • plate_shape (tuple[int, int] | Literal['infer']) – Tuple with the shape of the plate as (nrows, ncols) or None. If None, only one well is assumed. (Default: (8, 12))

  • well_shape (tuple[int, int]) – Tuple with the shape of the well as (nrows, ncols). (Default: (5, 5))

  • channel (int) – Channel to plot (default: 0, often is DAPI).

  • time (int) – Time slice to select (default: 0).

  • zaxis (int) – Slice along the Z-axis to take (default: 0).

  • well_layout (int) – Integer representing the order of tile capture (e.g., 9 is snake top to bottom). (Default: 9)

  • vmax (Literal[''] | int | None) – vmax to be passed to all imshow calls.

  • vmin (Literal[''] | int | None) – vmin to be passed to all imshow calls.

  • full_well (Literal['infer'] | ~collections.abc.Sequence[int] | dict[int | str, ~collections.abc.Sequence[int]] | None) – Optional sequence of the number of tiles per row in an elliptical well (e.g., Nikon elements tiling). If each well has a different shape, a dictionary can be provided, with the well name as the key and the sequence of the number of arow as values. Alternatively, ‘infer’ can be provided if the tile positions are available in the image metadata. If not provided (None, the default) is assumed to be a square.

  • max_workers (int) – Number of CPUs to use in inferring coordinates. Only used if full_well is infer.

  • kwargs – All additional keyword arguments are passed to the ~matplotlib.pyplot.subplots call.

Returns:

The matplotlib Figure containing the plot.