neuralib.scan.core.AbstractScanner

class neuralib.scan.core.AbstractScanner[source]

Bases: object

Abstract Base Class for confocal microscopy image data loaders.

Provides a common interface for accessing metadata and image data from various confocal file formats

__init__(filepath)[source]

Parameters:: filepath (str | Path | PathLike[str])

Methods

`__init__`(filepath)
`close`()	Explicitly close any open resources associated with the scanner.
`get_channel_names`(scene_idx)	Get the names of the fluorescence channels for a specific scene.
`view`(**kwargs)	view the 2D imaging array.
`z_projection`(stacks[, project_type, axis])	Computes a z-projection of a stack of images along a specified axis using a chosen method of projection.

Attributes

`dimcode`	Get dimension code for the image array
`filepath`	The absolute path to the loaded confocal file.
`metadata`	Return the metadata dictionary parsed from the file.
`n_scenes`	Total number of scenes (positions/series) in the file.

__init__(filepath)[source]

Parameters:: filepath (str | Path | PathLike[str])

close()[source]: Explicitly close any open resources associated with the scanner. Subclasses should override this if they open files or other resources.

property filepath: Path: The absolute path to the loaded confocal file.

property metadata: dict[str, Any]: Return the metadata dictionary parsed from the file.

abstract property dimcode: str: Get dimension code for the image array

abstract property n_scenes: int: Total number of scenes (positions/series) in the file.

abstractmethod get_channel_names(scene_idx)[source]

Get the names of the fluorescence channels for a specific scene.

Parameters:: scene_idx (int) – The 0-based index of the scene.
Returns:: A list of strings representing the channel names. Returns generic names (e.g., [‘Channel 1’, ‘Channel 2’]) if specific names are not available.
Raises:: IndexError – If scene_idx is out of bounds.
Return type:: list[str]

abstractmethod view(**kwargs)[source]

view the 2D imaging array. :return: A NumPy image array for view. Array[Any, [X, Y]]

Return type:: ndarray

static z_projection(stacks, project_type='max', axis=0)[source]

Computes a z-projection of a stack of images along a specified axis using a chosen method of projection. The function provides flexibility to select different projection types such as average, maximum, minimum, standard deviation, or median. The default projection type is max.

Parameters:

stacks (ndarray) – A multidimensional NumPy array representing the stack of images for z-projection.
project_type (Literal['avg', 'max', 'min', 'std', 'median']) – The type of projection to perform. Accepted values are: ‘avg’, ‘max’, ‘min’, ‘std’, or ‘median’. The default is ‘max’.
axis (int) – The axis along which the projection will be calculated. This is generally set according to the stack structure. Default is 0.

Returns:

A NumPy array containing the result of the z-projection along the specified axis.

Raises:

ValueError – If the given project_type is not one of the accepted values.

Return type:

ndarray