Read MM TIFF sequence

class iohub._deprecated.singlepagetiff.MicromanagerSequenceReader(folder, extract_data=False)

get_array(position)

return a numpy array for a given position

Parameters:

position: (int) position (aka ome-tiff scene)

Returns:

position: (np.ndarray)

get_image(p: int, t: int, c: int, z: int)

Get the image slice at dimension P, T, C, Z.

Parameters:

pint

index of the position dimension

tint

index of the time dimension

cint

index of the channel dimension

zint

index of the z dimension

Returns:

NDArray

2D image frame

get_num_positions()

get total number of scenes referenced in ome-tiff metadata

Returns:

number of positions (int)

get_zarr(position)

return a zarr array for a given position

Parameters:

position: (int) position (aka ome-tiff scene)

Returns:

position: (zarr.array)

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’)

read_tiff_series(folder: str)

given a folder containing position subfolders, each of which contains single-page-tiff series acquired using micro-manager, parse the metadata to map image coordinates to filepaths/names

Parameters:

folder: (str)

project folder containing all position subfolders

Returns:

coord_filename_map (dict)

keys are coordinates and values are filenames. Coordinates follow (p, t, c, z) indexing.

property shape

Get the underlying data shape as a tuple.

Returns:

tuple

(frames, slices, channels, height, width)