Light-field fluorescence microscopy(LFM)is a powerful elegant compact method for long-term highspeed imaging of complex biological systems,such as neuron activities and rapid movements of organelles.LFM experiments ty...Light-field fluorescence microscopy(LFM)is a powerful elegant compact method for long-term highspeed imaging of complex biological systems,such as neuron activities and rapid movements of organelles.LFM experiments typically generate terabytes of image data and require a substantial amount of storage space.Some lossy compression algorithms have been proposed recently with good compression performance.However,since the specimen usually only tolerates low-power density illumination for longterm imaging with low phototoxicity,the image signal-to-noise ratio(SNR)is relatively low,which will cause the loss of some efficient position or intensity information using such lossy compression algorithms.Here,we propose a phase-space continuity-enhanced bzip2(PC-bzip2)lossless compression method for LFM data as a high-efficiency and open-source tool that combines graphics processing unit-based fast entropy judgment and multicore-CPU-based high-speed lossless compression.Our proposed method achieves almost 10%compression ratio improvement while keeping the capability of high-speed compression,compared with the original bzip2.We evaluated our method on fluorescence beads data and fluorescence staining cells data with different SNRs.Moreover,by introducing temporal continuity,our method shows the superior compression ratio on time series data of zebrafish blood vessels.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.62371006,61931008,U21B2024,and 62071415)the National Key Research and Development Program of China(Grant No.2020YFB1406604)+2 种基金the Zhejiang Provincial Natural Science Foundation of China(Grant Nos.LDT23F01011F01,LDT23F01015F01,and LDT23F01014F01)the“Pioneer”and“Leading Goose”R&D Program of Zhejiang Province(Grant No.2022C01068)the China Postdoctoral Science Foundation(Grant Nos.2023TQ0006 and GZC20230057).
文摘Light-field fluorescence microscopy(LFM)is a powerful elegant compact method for long-term highspeed imaging of complex biological systems,such as neuron activities and rapid movements of organelles.LFM experiments typically generate terabytes of image data and require a substantial amount of storage space.Some lossy compression algorithms have been proposed recently with good compression performance.However,since the specimen usually only tolerates low-power density illumination for longterm imaging with low phototoxicity,the image signal-to-noise ratio(SNR)is relatively low,which will cause the loss of some efficient position or intensity information using such lossy compression algorithms.Here,we propose a phase-space continuity-enhanced bzip2(PC-bzip2)lossless compression method for LFM data as a high-efficiency and open-source tool that combines graphics processing unit-based fast entropy judgment and multicore-CPU-based high-speed lossless compression.Our proposed method achieves almost 10%compression ratio improvement while keeping the capability of high-speed compression,compared with the original bzip2.We evaluated our method on fluorescence beads data and fluorescence staining cells data with different SNRs.Moreover,by introducing temporal continuity,our method shows the superior compression ratio on time series data of zebrafish blood vessels.
