Read NDTiff#
- class iohub.ndtiff.NDTiffDataset(data_path: Path | str)[source]#
Reader for ND-TIFF datasets acquired with Micro/Pycro-Manager, effectively a wrapper of the ndtiff.Dataset class.
- get(k[, d]) D[k] if k in D, else d. d defaults to None.#
- get_image_metadata(p: int | str, t: int, c: int | str, z: int) dict[source]#
Return image plane metadata at the requested PTCZ coordinates
- Parameters:
- pint or str
position index
- tint
time index
- cint or str
channel index
- zint
slice/z index
- Returns:
- dict
image plane metadata
- 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.
- property root: Path#
Root directory of the dataset.
- property str_channel_axis: bool#
Channel axis is string-valued
- property str_position_axis: bool#
Position axis is string-valued
- values() an object providing a view on D's values#
- property zyx_scale: tuple[float, float, float]#
ZXY pixel size in micrometers.
- class iohub.ndtiff.NDTiffFOV(parent: NDTiffDataset, key: int)[source]#
- channel_index(key: str) int#
Return index of given channel.
- frame_metadata(t: int, c: int, z: int) dict[str, Any][source]#
Return image plane metadata for a given camera frame.
- Parameters:
- tint
Time index.
- zint
Z slice index.
- cint
Channel index.
- Returns:
- dict | None
Image plane metadata. None if not available.
- 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).