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Light-field fluorescence microscopy (LFM) is a powerful elegant compactmethod for long-term high-speed imaging of complex biological systems, such asneuron activities and rapid movements of organelles. LFM experiments typicallygenerate terabytes image data and require a huge number of storage space. Somelossy compression algorithms have been proposed recently with good compressionperformance. However, since the specimen usually only tolerates low powerdensity illumination for long-term imaging with low phototoxicity, the imagesignal-to-noise ratio (SNR) is relative-ly low, which will cause the loss ofsome efficient position or intensity information by using such lossycompression al-gorithms. Here, we propose a phase-space continuity enhancedbzip2 (PC-bzip2) lossless compression method for LFM data as a high efficiencyand open-source tool, which combines GPU-based fast entropy judgement andmulti-core-CPU-based high-speed lossless compression. Our proposed methodachieves almost 10% compression ratio improvement while keeping the capabilityof high-speed compression, compared with original bzip2. We evaluated ourmethod on fluorescence beads data and fluorescence staining cells data withdifferent SNRs. Moreover, by introducing the temporal continuity, our methodshows the superior compression ratio on time series data of zebrafish bloodvessels.

PC-bzip2: a phase-space continuity enhanced lossless compression algorithm for light field microscopy data