BrukerTiffImagingExtractors#

ImagingExtractors for the TIFF image format produced by Bruker.

Classes#

BrukerTiffSinglePlaneImagingExtractor

A ImagingExtractor for TIFF files produced by Bruker with only 1 plane.

BrukerTiffMultiPlaneImagingExtractor

A MultiImagingExtractor for TIFF files produced by Bruker with multiple planes.

filter_read_uic_tag_warnings(record)[source]#

Filter out the warnings from tifffile.read_uic_tag() that are not relevant to the user.

class BrukerTiffMultiPlaneImagingExtractor(folder_path: str | Path, stream_name: str | None = None)[source]#

Bases: MultiImagingExtractor

A MultiImagingExtractor for TIFF files produced by Bruke with multiple planes.

This format consists of multiple TIF image files (.ome.tif) and configuration files (.xml, .env).

Create a BrukerTiffMultiPlaneImagingExtractor instance from a folder path that contains the image files.

Parameters:

  • folder_path (PathType) – The path to the folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env).

  • stream_name (str, optional) – The name of the recording channel (e.g. “Ch2”).

Raises:

  • ValueError – If more than one recording stream is detected.

  • ValueError – If the selected stream is not in the available plane_streams.

  • AssertionError – If the TIF image files are missing from the folder.

  • AssertionError – If the imaging is not volumetric.

classmethod get_streams(folder_path: str | Path) → dict[source]#

Get the available streams from the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env).

Parameters:

folder_path (PathType) – The path to the folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env).

Returns:

streams – The dictionary of available streams.

Return type:

dict

get_image_shape() → tuple[int, int][source]#

Get the shape of the video frame (num_rows, num_columns).

Returns:

image_shape – Shape of the video frame (num_rows, num_columns).

Return type:

tuple

get_num_samples() → int[source]#

Get the number of samples in the video.

Returns:

num_samples – Number of samples in the video.

Return type:

int

get_sampling_frequency() → float[source]#

Get the sampling frequency in Hz.

Returns:

sampling_frequency – Sampling frequency in Hz.

Return type:

float

get_series(start_sample: int | None = None, end_sample: int | None = None) → ndarray[source]#

Get the video frames.

Parameters:

  • start_sample (int, optional) – Start sample index (inclusive).

  • end_sample (int, optional) – End sample index (exclusive).

Returns:

series – The video frames.

Return type:

numpy.ndarray

get_num_planes() → int[source]#

Get the number of depth planes.

Returns:

num_planes – The number of depth planes.

Return type:

int

get_volume_shape() → tuple[int, int, int][source]#

Get the shape of the volumetric video (num_rows, num_columns, num_planes).

Returns:

video_shape – Shape of the volumetric video (num_rows, num_columns, num_planes).

Return type:

tuple

class BrukerTiffSinglePlaneImagingExtractor(folder_path: str | Path, stream_name: str | None = None)[source]#

Bases: MultiImagingExtractor

A MultiImagingExtractor for TIFF files produced by Bruker with only 1 plane.

Create a BrukerTiffSinglePlaneImagingExtractor instance from a folder path that contains the image files.

Parameters:

  • folder_path (PathType) – The path to the folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env).

  • stream_name (str, optional) – The name of the recording channel (e.g. “Ch2” or “Green”).

classmethod get_streams(folder_path: str | Path) → dict[source]#

Get the available streams from the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env).

Parameters:

folder_path (PathType) – The path to the folder that contains the Bruker TIF image files (.ome.tif) and configuration files (.xml, .env).

Returns:

streams – The dictionary of available streams.

Return type:

dict

static get_available_channels(folder_path: str | Path) → set[str][source]#

Extract set of available channel names from the XML configuration file in the specified folder.

Parameters:

folder_path (PathType) – The path to the folder containing the XML configuration file. It can be either a string or a Path object.

Returns:

A set of channel names available in the first ‘Frame’ element found in the XML configuration file.

Return type:

Set[str]

get_image_shape() → tuple[int, int][source]#

Get the shape of the video frame (num_rows, num_columns).

Returns:

image_shape – Shape of the video frame (num_rows, num_columns).

Return type:

tuple

get_sampling_frequency() → float[source]#

Get the sampling frequency in Hz.

Returns:

sampling_frequency – Sampling frequency in Hz.

Return type:

float

get_channel_names() → list[str][source]#

Get the channel names in the recoding.

Returns:

channel_names – List of strings of channel names

Return type:

list

get_dtype() → dtype[Any] | None | type[Any] | _SupportsDType[dtype[Any]] | str | tuple[Any, int] | tuple[Any, SupportsIndex | Sequence[SupportsIndex]] | list[Any] | _DTypeDict | tuple[Any, Any][source]#

Get the data type of the video.

Returns:

dtype – Data type of the video.

Return type:

dtype