Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers

• Published in: Bioinformatics (Oxford, England) Vol. 35; no. 24; pp. 5393 - 5395
• Main Authors: Wait, Eric, Winter, Mark, Cohen, Andrew R
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.12.2019
• Subjects: Algorithms; Applications Notes; Computers; Gene Library; Software
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/btz523

Light microscopes can now capture data in five dimensions at very high frame rates producing terabytes of data per experiment. Five-dimensional data has three spatial dimensions (x, y, z), multiple channels (λ) and time (t). Current tools are prohibitively time consuming and do not efficiently utilize available hardware. The hydra image processor (HIP) is a new library providing hardware-accelerated image processing accessible from interpreted languages including MATLAB and Python. HIP automatically distributes data/computation across system and video RAM allowing hardware-accelerated processing of arbitrarily large images. HIP also partitions compute tasks optimally across multiple GPUs. HIP includes a new kernel renormalization reducing boundary effects associated with widely used padding approaches. HIP is free and open source software released under the BSD 3-Clause License. Source code and compiled binary files will be maintained on http://www.hydraimageprocessor.com. A comprehensive description of all MATLAB and Python interfaces and user documents are provided. HIP includes GPU-accelerated support for most common image processing operations in 2-D and 3-D and is easily extensible. HIP uses the NVIDIA CUDA interface to access the GPU. CUDA is well supported on Windows and Linux with macOS support in the future.