Read PTI TIFF#
- class iohub._deprecated.upti.UPTIReader(folder: str, extract_data: bool = False)[source]#
Reader for UPTI raw data. Accepts both new live UPTI and older UPTI format.
- get_array(position)[source]#
return a numpy array for a given position. Allows for only one position
- Parameters:
- position: (int) position
- Returns:
- position: (np.ndarray)
- get_image(p: int, t: int, c: int, z: int) ndarray[Any, dtype[_ScalarType_co]]#
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() int[source]#
Get total number of scenes referenced in ome-tiff metadata.
- Returns:
- int
number of positions
- get_zarr(position)[source]#
return a zarr array for a given position. Allows for only one position
- Parameters:
- position: (int) position
- 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’)
- property shape#
Get the underlying data shape as a tuple.
- Returns:
- tuple
(frames, slices, channels, height, width)