neuralib.scan.czi.CziScanner

final class neuralib.scan.czi.CziScanner[source]

Bases: AbstractScanner

CZI confocal image data

__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.
`get_code`(scene_idx, code)	Retrieves a specific shape value associated with a given scene index and access code from the internal czi_file data structure.
`get_tile_info`([scene_idx])	Extracts tile region information from metadata, if available.
`view`([scene, channel, depth, project_type, norm])	Generates a view of the image data based on the provided parameters such as scene, channel, depth, projection type, and normalization.
`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

`consistent_config`	Checks if the CZI file have consistent scanning configs across scenes
`czi_file`	get `aicspylibczi.CziFile` object
`dimcode`	Get dimension code for the image array
`filepath`	The absolute path to the loaded confocal file.
`is_mosaic`	Checks if the CZI file is marked as mosaic by the reader.
`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 czi_file: CziFile: get aicspylibczi.CziFile object

property consistent_config: bool: Checks if the CZI file have consistent scanning configs across scenes

property is_mosaic: bool: Checks if the CZI file is marked as mosaic by the reader.

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

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

get_code(scene_idx, code)[source]

Retrieves a specific shape value associated with a given scene index and access code from the internal czi_file data structure.

Parameters:

scene_idx (int) – The index representing a specific scene in the czi_file’s dimensions.
code (Literal['S', 'C', 'Z', 'X', 'Y', 'M']) – A string key for accessing a particular value related to the given scene index.

Returns:

Returns the shape value corresponding to the scene index and code

Return type:

int

get_tile_info(scene_idx=0)[source]

Extracts tile region information from metadata, if available. Returns None if not a tiled acquisition or info is missing

Parameters:: scene_idx (int)
Return type:: dict[str, Any] | None

get_channel_names(scene_idx)[source]

Get the names of the fluorescence channels for a specific scene. (Implementation copied from czi_scanner_impl_v1 for completeness)

Parameters:: scene_idx (int)
Return type:: list[str]

view(scene=None, channel=0, depth=None, project_type='max', norm=True, **kwargs)[source]

Generates a view of the image data based on the provided parameters such as scene, channel, depth, projection type, and normalization. The function retrieves image data from either a mosaic file or a standard image file, processes it according to the specified depth, performs projection if required, and applies normalization if requested.

Parameters:

scene (int | None) – Scene index to be used for image loading. If None and the file is non-mosaic, defaults to 0. Used only for non-mosaic CZI files.
channel (int) – Index of the channel to be visualized. Defaults to 0.
depth (int | slice | ndarray | None) – Z-plane depth index, slice, or array. If None, all Z-slices are loaded. Can also be a specific integer index or an array of indices/slice.
project_type (Literal['avg', 'max', 'min', 'std', 'median']) – Type of Z-projection to apply if multiple Z-slices are selected. Options include ‘avg’, ‘max’, ‘min’, ‘std’, ‘median’. Defaults to ‘max’.
norm (bool) – Whether to normalize the image intensity values. If True, divides the data by its maximum intensity value. Defaults to True.
kwargs (Any)

Returns:

A NumPy array containing the processed image data, which may be normalized and/or projected based on the input parameters.

Return type:

ndarray