tiffwrite 2022.5.2

Parallel tiff writer compatible with ImageJ.

Tiffwrite

Exploiting tifffile in parallel to write BioFormats/ImageJ compatible tiffs with good compression.

Features

• Writes bigtiff files that open in ImageJ as hyperstack with correct dimensions.
• Parallel compression.
• Write individual frames in random order.
• Compresses even more by referencing tag or image data which otherwise would have been saved several times. For example empty frames, or a long string tag on every frame.
• Enables memory efficient scripts by saving frames whenever they're ready to be saved, not waiting for the whole stack.
• Colormaps, extra tags globally or frame dependent.

Installation

pip install tiffwrite

or

pip install tiffwrite@git+https://github.com/wimpomp/tiffwrite

Usage

Write an image stack

tiffwrite(file, data, axes='TZCXY', dtype=None, bar=False, *args, **kwargs)

• file: string; filename of the new tiff file.
• data: 2 to 5D numpy array in one of these datatypes: (u)int8, (u)int16, float32.
• axes: string; order of dimensions in data, default: TZCXY for 5D, ZCXY for 4D, CXY for 3D, XY for 2D data.
• dtype: string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported.
• bar: bool; whether or not to show a progress bar.
• args, kwargs: arguments to be passed to IJTiffFile, see below.

Write one frame at a time

with IJTiffFile(file, shape, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None,
                timeinterval=None, **extratags) as tif:
some loop:
    tif.save(frame, c, z, t)

• file: string; filename of the new tiff file.

• shape: iterable; shape (C, Z, T) of data to be written in file.

• dtype: string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported.

• colors: iterable of strings; one color per channel, valid colors (also html) are defined in matplotlib.colors. Without colormap BioFormats will set the colors in this order: rgbwcmy. Note that the color green is dark, the usual green is named 'lime' here.

• colormap: string; choose any colormap from the colorcet module. Colors and colormap cannot be used simultaneously.

• pxsize: float; pixel size im um.

• deltaz: float; z slice interval in um.

• timeinterval: float; time between frames in seconds.

• extratags: other tags to be saved, example: Artist='John Doe', Tag4567=[400, 500] or Copyright=Tag('ascii', 'Made by me'). See tiff_tag_registry.items().

• frame: 2D numpy array with data.

• c, z, t: int; channel, z, time coordinates of the frame.

Examples

Write an image stack

from tiffwrite import tiffwrite
import numpy as np

image = np.random.randint(0, 255, (5, 3, 64, 64), 'uint16')
tiffwrite('file.tif', image, 'TCXY')

Write one frame at a time

from itertools import product
from tiffwrite import IJTiffFile
import numpy as np

shape = (3, 5, 10)  # channels, z, time
with IJTiffFile('file.tif', shape, pxsize=0.09707) as tif:
    for c in range(shape[0]):
        for z in range(shape[1]):
            for t in range(shape[2]):
                tif.save(np.random.randint(0, 10, (32, 32)), c, z, t)

Saving multiple tiffs simultaneously

from itertools import product
from tiffwrite import IJTiffFile
import numpy as np

shape = (3, 5, 10)  # channels, z, time
with IJTiffFile('fileA.tif', shape) as tif_a, IJTiffFile('fileB.tif', shape) as tif_b:
    for c in range(shape[0]):
        for z in range(shape[1]):
            for t in range(shape[2]):
                tif_a.save(np.random.randint(0, 10, (32, 32)), c, z, t)
                tif_b.save(np.random.randint(0, 10, (32, 32)), c, z, t)

Tricks & tips

• The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order de ifd's such that the file will be opened as a correctly ordered hyperstack.
• Using the colormap parameter you can make ImageJ open the file and apply the colormap. colormap='glasbey' is very useful.
• IJTiffFile does not allow more than one pool of parallel processes to be open at a time. Therefore, when writing multiple tiff's simultaneously you have to open all before you start saving any frame, in this way all files share the same pool.