cpp-tiff

An efficient parallel Tiff reader/writer that utilizes LibTIFF and OpenMP.

Limitations

1. Currently RGB tiffs are not supported but support may be added in the future

Python

A Python version of cpp-tiff is available through pip

Prerequisites

Python

Python version >=3.8

OS

Linux: All Linux distros made within the past 10 years should work

Mac Apple Silicon (M1, M2, etc.): macOS 13 or newer is required

Mac Intel: macOS 12 or newer is required

Windows: Windows 10 or newer is required

Installation

pip install cpp-tiff

Usage

The reader returns a zyx numpy array for the given tiff file

The writer takes an output filename and a zyx numpy array

By default, the writer uses lzw compression but you can also pass 'none' as the third argument

Read and Write a tiff file

import cpptiff
im = cpptiff.read_tiff('filename.tif')
# Do some processing here
cpptiff.write_tiff('outputFilename.tif', im)

Get the shape of a tiff file without reading the image

import cpptiff
im_shape = cpptiff.get_image_shape('filename.tif')

CMake

The C++ library can be compiled using the CMakeLists.txt file

Prerequisites

1. Dependencies are included in the dependencies folder
2. Currently the only officially supported compiler is gcc on Linux and Mac and MinGW on Windows but others may work

Download and Install

git clone https://github.com/abcucberkeley/cpp-zarr
cd cpp-zarr
mkdir build
cd build
cmake ..
make -j
make install

MATLAB

Prerequisites

1. None! The parallel reader and writer mex files will work with the most recent version of Matlab.

Download and Install

1. Download the latest release for your OS from here: https://github.com/abcucberkeley/cpp-tiff/releases
2. Unzip the folder
3. You can now put the mex files wherever you'd like and add them to your path if needed
4. Note for Mac Users: You may need to restart Matlab before using the Mex files if you have an open session

Usage

getImageSizeMex - Get the dimensions of a Tiff image

size = getImageSizeMex('path/to/file.tif');

parallelReadTiff - Read a Tiff image into an array

im = parallelReadTiff('path/to/file.tif');

parallelWriteTiff - Write an array out as a Tiff image

im = rand(100,100,100);
parallelWriteTiff('path/to/file.tif',im);

Reference

Please cite our software if you find it useful in your work:

Xiongtao Ruan, Matthew Mueller, Gaoxiang Liu, Frederik Görlitz, Tian-Ming Fu, Daniel E. Milkie, Joshua L. Lillvis, Alexander Kuhn, Chu Yi Aaron Herr, Wilmene Hercule, Marc Nienhaus, Alison N. Killilea, Eric Betzig, Srigokul Upadhyayula. Image processing tools for petabyte-scale light sheet microscopy data. Nature Methods (2024). https://doi.org/10.1038/s41592-024-02475-4