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Updated: Aug 3, 2025

Single Particle Cryo-Electron Microscopy: From Sample to Structure
Published on: May 29, 2021
Progressive Tree-Based Compression of Large-Scale Particle Data
Abstract:
Scientific simulations and observations using particles have been creating large datasets that require effective and efficient data reduction to store, transfer, and analyze. However, current approaches either compress only small data well while being inefficient for large data, or handle large data but with insufficient compression. Toward effective and scalable compression/decompression of particle positions, we introduce new kinds of particle hierarchies and corresponding traversal orders that quickly reduce reconstruction error while being fast and low in memory footprint. Our solution to compression of large-scale particle data is a flexible block-based hierarchy that supports progressive, random-access, and error-driven decoding, where error estimation heuristics can be supplied by the user. For low-level node encoding, we introduce new schemes that effectively compress both uniform and densely structured particle distributions. Our proposed methods thus target all three phases of a tree-based particle compression pipeline, namely tree construction, tree traversal, and node encoding. The improved efficacy and flexibility of these methods over existing compressors are demonstrated through extensive experimentation, using a wide range of scientific particle datasets.
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