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Published July 6, 2024 | Version v2
Software Open

Benchmark Code for the Paper "Image Processing Tools for Petabyte-Scale Light Sheet Microscopy Data"

Authors/Creators

  • 1. ROR icon University of California, Berkeley

Description

Code to replicate the benchmark results in the paper "Image processing tools for petabyte-scale light sheet microscopy data".

The code is kept as it is for the benchmarks in a Linux computing cluster. For details, please refer to the readme.txt in the zip file and the paper. It includes a small image (512x1800x500) in Zarr format to generate benchmark data for Tiff and Zarr readers and writers, as well as for deskew/rotation benchmarks. We also included a copy of the PetaKit5D software used for the benchmarks.

Please cite our paper (https://doi.org/10.1101/2023.12.31.573734) if you find the software useful for your research:

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

Files

PetaKit5D_paper_benchmark_code.zip

Files (459.2 MB)

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md5:9be9121ab2c776768b9ff27568fd003a
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Additional details

Identifiers

DOI
10.1101/2023.12.31.573734

Related works

Cites
Publication: 10.1101/2023.12.31.573734 (DOI)
Is supplement to
Software: https://github.com/abcucberkeley/PetaKit5D (URL)
Software: https://github.com/abcucberkeley/PetaKit5D-GUI (URL)
Software: https://github.com/abcucberkeley/Parallel_Fiji_Visualizer (URL)
Software: https://github.com/abcucberkeley/PyPetaKit5D (URL)

References

  • 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