Light-field fluorescence microscopy (LFM) is a powerful elegant compact method for long-term high-speed 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 long-term 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.

Micro-endoscopes are widely used for detecting and visualizing hard-to-reach areas of the human body and for in vivo observation of animals. A micro-endoscope that can realize 3D imaging at the camera framerate could benefit various clinical and biological applications. In this work, we report the development of a compact light-field micro-endoscope (LFME) that can obtain snapshot 3D fluorescence imaging, by jointly using a single-mode fiber bundle and a small-size light-field configuration. To demonstrate the real imaging performance of our method, we put a resolution chart in different z positions and capture the z-stack images successively for reconstruction, achieving 333-μm-diameter field of view, 24 μm optimal depth of field, and up to 3.91 μm spatial resolution near the focal plane. We also test our method on a human skin tissue section and HeLa cells. Our LFME prototype provides epi-fluorescence imaging ability with a relatively small (2-mm-diameter) imaging probe, making it suitable for in vivo detection of brain activity and gastrointestinal diseases of animals.