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

Quick Start Guide (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);

Compiling with 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

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. bioRxiv 2023.12.31.573734; doi: https://doi.org/10.1101/2023.12.31.573734