Adding `tiffwrite` library as a dependency

Run this command in a terminal, in your project's directory:

cargo add tiffwrite

To add it manually, edit your project's Cargo.toml file and add to the [dependencies] section:

tiffwrite = "2025.12.0"

The tiffwrite library will be automatically available globally. Read the tiffwrite library documentation.

Back to the crate overview.

Readme

Tiffwrite

Write BioFormats/ImageJ compatible tiffs with zstd compression in parallel using Rust.

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. Editing tiffs becomes mostly impossible, but compression makes that very hard anyway.
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.

Python

Installation

pip install tiffwrite

install rust
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 to show a progress bar.
args, kwargs: arguments to be passed to IJTiffFile, see below.

Write one frame at a time

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

path: string; path to the new tiff file.
dtype: string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported by Fiji.
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.
compression: int; zstd compression level: -7 to 22.
comment: str; comment to be saved in tif
extratags: Sequence[Tag]; other tags to be saved, example: Tag.ascii(315, 'John Doe') or Tag.ascii(33432, 'Made by me').
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 tiffwrite import IJTiffFile
import numpy as np

with IJTiffFile('file.tif', pxsize=0.09707) as tif:
    for c in range(3):
        for z in range(5):
            for t in range(10):
                tif.save(np.random.randint(0, 10, (32, 32)), c, z, t)

Saving multiple tiffs simultaneously

from tiffwrite import IJTiffFile
import numpy as np

with IJTiffFile('fileA.tif') as tif_a, IJTiffFile('fileB.tif') as tif_b:
    for c in range(3):
        for z in range(5):
            for t in range(10):
                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)

Rust

use ndarray::Array2;
use tiffwrite::IJTiffFile;

{  // f will be closed when f goes out of scope
    let mut f = IJTiffFile::new("file.tif")?;
    for c in 0..3 {
        for z in 0..5 {
            for t in 0..10 {
                let arr = Array2::<u16>::zeros((100, 100));
                f.save(&arr, c, z, t)?;
            }
        }
    }
}

Tricks & tips

The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order the 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.

Adding tiffwrite library as a dependency

Adding `tiffwrite` library as a dependency