scallops.io.save_stack_imagej

scallops.io.save_stack_imagej(uri, data, luts=None, display_ranges=None, resolution=1.0, compress=0, dimensions=None, display_mode='composite')

Taken and modified from https://github.com/blaineylab/OpticalPooledScreens.

Saves data as tiff file with imageJ compatibility.

Parameters:

  • uri (str) – Path or url to store the tiff file

  • data (ndarray) – an array with 5, 4, 3, or 2 dimensions [TxZxCxYxX]

  • luts (tuple[Sequence[int], ...] | None) – ImageJ lookup table for each channel (e.g, scallops.io.GRAY, scallops.io.GREEN, etc)

  • display_ranges (tuple[tuple[int, int], ...] | None) – The display range can be set with a list of (min, max) pairs for each channel.

  • resolution (float) – Resolution of the image in microns per pixel

  • compress (Literal[0, 1]) – Compress the image. Setting to 1 saves a lot of space for integer masks

  • dimensions (str) – Dimensionality of the data. Leading dimenstions in order (i.e. TCZ, TC, CT)

  • display_mode (Literal['composite', 'color', 'grayscale']) – Sets the display mode, where mode is “composite”, “color” or “grayscale”

>>> random_data = np.random.randint(0, 2**16, size=(3, 100, 100), dtype=np.uint16)
>>> ramp = list(range(256))
>>> ZERO = [0] * 256
>>> RED = ramp + ZERO + ZERO
>>> GREEN = ZERO + ramp + ZERO
>>> BLUE = ZERO + ZERO + ramp
>>> luts = GREEN, RED, BLUE
>>> display_ranges = (0, 60000), (0, 40000), (0, 20000)
>>> save_stack_imagej(
...     "random_image.tiff", random_data, luts=luts, display_ranges=display_ranges
... )
Compatible array data types are:

bool (converted to uint8 0, 255) uint8 uint16 float32 float64 (converted to float32)