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://git.pomppervova.nl/wim/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.

Metadata

Release files for tiffwrite 2026.6.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for tiffwrite 2026.6.0
File	Size	Uploaded
tiffwrite-2026.6.0.tar.gz	35.5 kB	Jun 16, 2026	Details

Built distributions (wheels)

Table of built distributions (wheels) for tiffwrite 2026.6.0
File	Interpreter	ABI	Platform	Reset
tiffwrite-2026.6.0-cp310-abi3-win_arm64.whl 1.7 MB Jun 16, 2026	CPython 3.10	abi3	Windows ARM64	Details
tiffwrite-2026.6.0-cp310-abi3-win_amd64.whl 1.8 MB Jun 16, 2026	CPython 3.10	abi3	Windows x86-64	Details
tiffwrite-2026.6.0-cp310-abi3-musllinux_1_2_x86_64.whl 2.0 MB Jun 16, 2026	CPython 3.10	abi3	Linux musl 1.2+ x86-64	Details
tiffwrite-2026.6.0-cp310-abi3-musllinux_1_2_aarch64.whl 1.9 MB Jun 16, 2026	CPython 3.10	abi3	Linux musl 1.2+ ARM64	Details
tiffwrite-2026.6.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 2.0 MB Jun 16, 2026	CPython 3.10	abi3	Linux glibc 2.17+ x86-64	Details
tiffwrite-2026.6.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 1.9 MB Jun 16, 2026	CPython 3.10	abi3	Linux glibc 2.17+ ARM64	Details
tiffwrite-2026.6.0-cp310-abi3-macosx_11_0_arm64.whl 3.2 MB Jun 16, 2026	CPython 3.10	abi3	macOS 11.0+ ARM64	Details
tiffwrite-2026.6.0-cp310-abi3-macosx_10_12_x86_64.whl 3.3 MB Jun 16, 2026	CPython 3.10	abi3	macOS 10.12+ x86-64	Details

Total release size: 17.9 MB

Release files / tiffwrite-2026.6.0.tar.gz

Download URL	tiffwrite-2026.6.0.tar.gz
Size	35.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`15ee6e1df6e1743084a091c238fd1f3f9fb7374e24c05254d04909ee06ae1b1b`
BLAKE2b-256 checksum How to use checksums	`abaeedb8bada7c1eb53bc2dc9aaa366815c7de05acec4f16ad3b09bb393afb19`
Upload date	Jun 16, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.2.0 CPython/3.13.13`

Release files / tiffwrite-2026.6.0-cp310-abi3-win_arm64.whl

Download URL	tiffwrite-2026.6.0-cp310-abi3-win_arm64.whl
Size	1.7 MB
Tags	CPython 3.10 Windows ARM64 abi3
SHA-256 checksum How to use checksums	`9d8af68324f2c2565ff45e31a33cf5fe6ea9f8eeb12bc64a21e60ef3f306c29f`
BLAKE2b-256 checksum How to use checksums	`365741645df36ca720ea43b3347df5d3f509ec297229ec91cb1c96827fa646d8`
Upload date	Jun 16, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.12`

Release files / tiffwrite-2026.6.0-cp310-abi3-win_amd64.whl

Download URL	tiffwrite-2026.6.0-cp310-abi3-win_amd64.whl
Size	1.8 MB
Tags	CPython 3.10 Windows x86-64 abi3
SHA-256 checksum How to use checksums	`60da8a3c078a2ad0d61ad84c7b80b13f925b5e936369ce43d9f68af58d9c85b9`
BLAKE2b-256 checksum How to use checksums	`18e8a43ffeab74bead7ea3573f7f2d483961824b700161dd0c7e24b21d4ac7eb`
Upload date	Jun 16, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.12`

Release files / tiffwrite-2026.6.0-cp310-abi3-musllinux_1_2_x86_64.whl

Download URL	tiffwrite-2026.6.0-cp310-abi3-musllinux_1_2_x86_64.whl
Size	2.0 MB
Tags	CPython 3.10 Linux musl 1.2+ x86-64 abi3
SHA-256 checksum How to use checksums	`5bedc6f07177f108c31f4bdb98a7fcf57ad4f1a44a2d79f04f88c8549fc739cf`
BLAKE2b-256 checksum How to use checksums	`1d774b90035230ffff0744cfad92587cc92618427a0e9225c63b468864891c8f`
Upload date	Jun 16, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.12`

Release files / tiffwrite-2026.6.0-cp310-abi3-musllinux_1_2_aarch64.whl

Download URL	tiffwrite-2026.6.0-cp310-abi3-musllinux_1_2_aarch64.whl
Size	1.9 MB
Tags	CPython 3.10 Linux musl 1.2+ ARM64 abi3
SHA-256 checksum How to use checksums	`1c1c8afb7e855cda5a22e02311270186bc1e7545415d3e88f85cf893e2b15151`
BLAKE2b-256 checksum How to use checksums	`15e7ae5c57f2956baa44b46ec44b96522431ad97be50a0f3527bf4d2666836c8`
Upload date	Jun 16, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.12`

Release files / tiffwrite-2026.6.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL	tiffwrite-2026.6.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Size	2.0 MB
Tags	CPython 3.10 Linux glibc 2.17+ x86-64 abi3
SHA-256 checksum How to use checksums	`808762329ccf2e1be0e6ce9e64dc584afc6fc3039ffa0abe76c4565e7f9631a2`
BLAKE2b-256 checksum How to use checksums	`311b39f73005e3cf0bcafd56e5c2e88fc5cf7a80db867f3d2dbd3601e91b7aa8`
Upload date	Jun 16, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.12`

Release files / tiffwrite-2026.6.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

Download URL	tiffwrite-2026.6.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
Size	1.9 MB
Tags	CPython 3.10 Linux glibc 2.17+ ARM64 abi3
SHA-256 checksum How to use checksums	`4b89e8319449beb9a0b91b8d7b4b487454f57ef30ca8b5521641a0c4c09dbb83`
BLAKE2b-256 checksum How to use checksums	`8258e637db3e54bd4ca1e9248bbef2c66e28e29478c62c3e82266dbefa90db8d`
Upload date	Jun 16, 2026
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Uploaded via	`twine/6.1.0 CPython/3.13.12`

Release files / tiffwrite-2026.6.0-cp310-abi3-macosx_11_0_arm64.whl

Download URL	tiffwrite-2026.6.0-cp310-abi3-macosx_11_0_arm64.whl
Size	3.2 MB
Tags	CPython 3.10 abi3 macOS 11.0+ ARM64
SHA-256 checksum How to use checksums	`aa993e42f9f27f3ad5b0b565a29d88d04760448c59b9f0d26bf605b219b99d2e`
BLAKE2b-256 checksum How to use checksums	`ee6ddfb9bb1a4644b7e88ae20f6b57a5716b47347c3166bd0f0c000766173b90`
Upload date	Jun 16, 2026
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Uploaded via	`twine/6.1.0 CPython/3.13.12`

Release files / tiffwrite-2026.6.0-cp310-abi3-macosx_10_12_x86_64.whl

Download URL	tiffwrite-2026.6.0-cp310-abi3-macosx_10_12_x86_64.whl
Size	3.3 MB
Tags	CPython 3.10 abi3 macOS 10.12+ x86-64
SHA-256 checksum How to use checksums	`c569636f0f7470d459b7b72c2f56dedb8817f075069ee30a83c6c7486a537bae`
BLAKE2b-256 checksum How to use checksums	`2ab287bbbf0d797eda981fb31a60d14411efe24732c466516fc0dfc880af4435`
Upload date	Jun 16, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.12`