MicroManagerTiffImagingExtractor#

class MicroManagerTiffImagingExtractor(folder_path: str | Path)[source]#

Bases: MultiImagingExtractor

Specialized extractor for reading TIFF files produced via Micro-Manager.

The image file stacks are saved into multipage TIF files in OME-TIFF format (.ome.tif files), each of which are up to around 4GB in size. The ‘DisplaySettings’ JSON file contains the properties of Micro-Manager.

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

Parameters:

folder_path (PathType) – The folder path that contains the multipage OME-TIF image files (.ome.tif files) and the ‘DisplaySettings’ JSON file.

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_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_channel_names() → list[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