Read MMStack OME-TIFF#

class iohub.mmstack.MMStack(data_path: StrOrBytesPath)[source]#

Micro-Manager multi-file OME-TIFF (MMStack) reader.

Parameters:

data_pathStrOrBytesPath: Path to the directory containing OME-TIFF files or the path to the first OME-TIFF file in the series

close() → None[source]#: Close file handles

get(k[, d]) → D[k] if k in D, else d. d defaults to None.#

property hcs_position_labels#

Parse plate position labels generated by the HCS position generator, e.g. ‘A1-Site_0’ or ‘1-Pos000_000’, and split into row, column, and FOV names.

Returns:

list[tuple[str, str, str]]: FOV name paths, e.g. (‘A’, ‘1’, ‘0’) or (‘0’, ‘1’, ‘000000’)

items() → a set-like object providing a view on D's items#

keys() → a set-like object providing a view on D's keys#

property micromanager_summary: dict | None#: Micro-manager summary metadata.

read_image_metadata(p: int, t: int, c: int, z: int) → dict | None[source]#: Read image plane metadata from the OME-TIFF file.

property root: Path#: Root directory of the dataset.

values() → an object providing a view on D's values#

property zyx_scale: tuple[float, float, float]#: ZXY pixel size in micrometers.

class iohub.mmstack.MMOmeTiffFOV(parent: MMStack, key: str)[source]#

channel_index(key: str) → int#: Return index of given channel.

frame_metadata(t: int, c: int, z: int) → dict | None[source]#: Read image plane metadata from the OME-TIFF file.

property t_scale: float#: Helper function for FOV time scale (seconds).

property zyx_scale: tuple[float, float, float]#: Helper function for FOV spatial scale (micrometer).