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Advancements in light microscopy have enabled neuroscience labs to employ fast, high-resolution imaging for whole-brain studies, generating vast amounts of raw data that require efficient stitching and reconstruction. Existing software struggles with handling terabyte-scale data, leading to memory and computational bottlenecks. To address these challenges, we present SmartStitcher, an intelligent tool designed to stitch ultra-large-scale (terabyte-level) microscopic data using the Mixed-Max-Resolution (MMR) approach. SmartStitcher optimizes the workflow by selectively retaining image tiles with neuronal information, reducing memory usage and computational load. It supports output in the TeraFly format and allows seamless transitions between different resolutions, enabling users to view whole-brain imaging at low resolution and zoom in on neuronal structures at high resolution. Encapsulated in a user-friendly graphical interface and available via command-line, SmartStitcher efficiently stitches large datasets within limited time and memory resources. The software is open-source and available on GitHub ( https://github.com/polya1998/SmartStitcher.git ).

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SmartStitcher: A Terabyte-Level 3D Microscopic Image Stitching Tool Based on Mixed-Max-Resolution

  • 会议论文

  • 发表日期：

    2025年

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  • Yabo Li,
  • Xiaoli Qi,
  • Liya Ding

摘要

Advancements in light microscopy have enabled neuroscience labs to employ fast, high-resolution imaging for whole-brain studies, generating vast amounts of raw data that require efficient stitching and reconstruction. Existing software struggles with handling terabyte-scale data, leading to memory and computational bottlenecks. To address these challenges, we present SmartStitcher, an intelligent tool designed to stitch ultra-large-scale (terabyte-level) microscopic data using the Mixed-Max-Resolution (MMR) approach. SmartStitcher optimizes the workflow by selectively retaining image tiles with neuronal information, reducing memory usage and computational load. It supports output in the TeraFly format and allows seamless transitions between different resolutions, enabling users to view whole-brain imaging at low resolution and zoom in on neuronal structures at high resolution. Encapsulated in a user-friendly graphical interface and available via command-line, SmartStitcher efficiently stitches large datasets within limited time and memory resources. The software is open-source and available on GitHub ( https://github.com/polya1998/SmartStitcher.git ).