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A real-time compression library for microscopy images

By Bálint Balázs, Joran Deschamps, Marvin Albert, Jonas Ries, Lars Hufnagel

Posted 21 Jul 2017
bioRxiv DOI: 10.1101/164624

Fluorescence imaging techniques such as single molecule localization microscopy, high-content screening and light-sheet microscopy are producing ever-larger datasets, which poses increasing challenges in data handling and data sharing. Here, we introduce a real-time compression library that allows for very fast (beyond 1 GB/s) compression and de-compression of microscopy datasets during acquisition. In addition to an efficient lossless mode, our algorithm also includes a lossy option, which limits pixel deviations to the intrinsic noise level of the image and yields compression ratio of up to 100-fold. We present a detailed performance analysis of the different compression modes for various biological samples and imaging modalities.

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