RT Journal Article
SR Electronic
T1 A real-time compression library for microscopy images
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 164624
DO 10.1101/164624
A1 Bálint Balázs
A1 Joran Deschamps
A1 Marvin Albert
A1 Jonas Ries
A1 Lars Hufnagel
YR 2017
UL http://biorxiv.org/content/early/2017/07/21/164624.abstract
AB 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.