Read MMStack OME-TIFF

class iohub.mmstack.MMStack(data_path: StrOrBytesPath)

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

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 and split them into (row, column, FOV) components.

This method supports multiple label formats commonly produced by micromanager. The returned values are a 3-part tuple with the following interpretation: - row: usually a letter (e.g. ‘A’), or ‘0’ if not explicitly given - column: the well column number or site index - fov: the field-of-view index, typically zero-padded

Supported label formats and their outputs:

Format → Output —————————– ———————- “A1-Site_0” → (‘A’, ‘1’, ‘0’) “1-Pos000_000” → (‘0’, ‘1’, ‘000000’) “2-Pos000_001” → (‘0’, ‘2’, ‘000001’) “1-Pos001” → (‘0’, ‘1’, ‘001000’) “Pos-5-000_005” → (‘0’, ‘5’, ‘000005’)

Returns:

list[tuple[str, str, str]]

A list of (row, column, fov) tuples corresponding to parsed label components in a uniform format.

Raises:

ValueError

If stage position metadata is missing or labels are not found.

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

Read image plane metadata from the OME-TIFF file.

property root: Path

Root directory of the dataset.

property t_scale: float

Time scale in seconds.

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)

channel_index(key: str) → int

Return index of given channel.

frame_metadata(t: int, c: int, z: int) → dict | None

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).