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This article introduces an analysis-aware microscopy video compression method designed for microscopy videos that are consumed by analysis algorithms rather than by the human visual system. We define the quality of a microscopy video based on the level of preservation of analysis results. We evaluated our method with a bead tracking analysis program. For the same error level in the analysis result, our method can achieve 1,000× compression on certain test microscopy videos. Compared with a previous technique that yields exactly the exact same results by analysis algorithms, our method gives more flexibility for a user to control the quality. A modification to the new method also provides faster compression speed., (© 2018 Wiley Periodicals, Inc.)

The large amount video data produced by multi-channel, high-resolution microscopy system drives the need for a new high-performance domain-specific video compression technique. We describe a novel compression method for video microscopy data. The method is based on Pearson's correlation and mathematical morphology. The method makes use of the point-spread function (PSF) in the microscopy video acquisition phase. We compare our method to other lossless compression methods and to lossy JPEG, JPEG2000, and H.264 compression for various kinds of video microscopy data including fluorescence video and brightfield video. We find that for certain data sets, the new method compresses much better than lossless compression with no impact on analysis results. It achieved a best compressed size of 0.77% of the original size, 25× smaller than the best lossless technique (which yields 20% for the same video). The compressed size scales with the video's scientific data content. Further testing showed that existing lossy algorithms greatly impacted data analysis at similar compression sizes., (© 2015 Wiley Periodicals, Inc.)