tiffwrite 2021.12.0

Parallel tiff writer compatible with ImageJ.

Tiffwrite

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

Features

• Writes bigtiff file that opens 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 save 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.

Installation

pip install tiffwrite

or

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

Usage

Write an image stack

tiffwrite(file, data, axes='TZCXY', bar=False, colormap=None, pxsize=None)

• 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.
• bar: bool; whether or not to show a progress bar.
• colormap: string; choose any colormap from the colorcet module.
• pxsize: float; set tiff tag so ImageJ can read the pixel size (in um).

Write one frame at a time

with IJTiffWriter(file, shape, dtype='uint16', colormap=None, nP=None, extratags=None, pxsize=None) as tif:
some loop:
    tif.save(frame, c, z, t)

• file: string; filename of the new tiff file, or list of filenames.

• 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.

• colormap: string; choose any colormap from the colorcet module.

• nP: int; number of compressor workers to use

• extratags: dict {int tagnr: (int type, data)}, extra tags to save on every frame, will cause a crash if not used correctly!

• pxsize: float; set tiff tag so ImageJ can read the pixel size (in um).

• 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 IJTiffWriter
import numpy as np

shape = (3, 5, 10)  # channels, z, time
with IJTiffWriter('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 IJTiffWriter
import numpy as np

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

Tricks & tips

• ImageJ colors channels in the order rgbwcym, and IJTiffwriter automatically and efficiently writes 0's when a frame is skipped. You can use this when specific colors are important, for example: you want to use only red and blue.
• The order of feeding frames to IJTiffWriter is unimportant, IJTiffWriter 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.