Data for: Image processing tools for petabyte-scale light sheet microscopy data (Part 1/2)

Light sheet microscopy is a powerful technique for high-speed 3D imaging of subcellular dynamics and large biological specimens. However, it often generates datasets ranging from hundreds of gigabytes to petabytes in size for a single experiment. Conventional computational tools process such images far slower than the time to acquire them and often fail outright due to memory limitations. To address these challenges, we present PetaKit5D, a scalable software solution for efficient petabyte-scale light sheet image processing. This software incorporates a suite of commonly used processing tools that are memory and performance-optimized. Notable advancements include rapid image readers and writers, fast and memory-efficient geometric transformations, high-performance Richardson-Lucy deconvolution, and scalable Zarr-based stitching. These features outperform state-of-the-art methods by over one order of magnitude, enabling the processing of petabyte-scale image data at the full teravoxel ra..., The light sheet, 2-photon, and phase images were collected with homemade light sheet, 2-photon, and oblique illumination \"phase\" microscopes. The widefield and confocal images were collected with Andor BC43 Benchtop Confocal Microscope (Oxford Instruments). The dataset has been processed with PetaKit5D (https://github.com/abcucberkeley/PetaKit5D)., , # Data for \"Image processing tools for petabyte-scale light sheet microscopy data (Part 1/2)\" --- The image data is organized for the figures in the paper \"Image processing tools for petabyte-scale light sheet microscopy data\" ([https://doi.org/10.1101/2023.12.31.573734](https://doi.org/10.1101/2023.12.31.573734)): ## Description of the data and file structure ### Schema of data archive ``` 20211003_Aang_largeFOV_11h_stepAndSettle.zip ├── 20211003_Aang_largeFOV_11h_stepAndSettle │  ├── flatfieldCorrection │  │  └── averaged │  │  ├── 488.tif │  │  └── 560.tif │  ├── PSF │  │  ├── 488_NA0p4_sig0p1_highSN.tif │  │  └── 560_NA0p4_sig0p1_highSN.tif │  └── run01 │  ├── ImageList_run01.csv │  ├── Scan_Iter_0000_000*_000x_00*y_000z_000*t_Settings.txt │  ├── Scan_Iter_0000_000*_CamA_ch0_CAM1_stack0000_488nm_0000000msec_0155431219msecAbs_000x_00*y_000z_000*t.tif │  └── Scan_Iter_0000_000*_CamB_ch0_CAM1_stack0000_488nm_0000000msec_0155431219msecAbs_00...光片显微镜（light sheet microscopy）是一种可实现亚细胞动态与大型生物标本高速三维成像的前沿技术。但单次实验即可产生数百吉字节至拍字节级别的数据集。传统计算工具处理此类图像的速度远慢于图像采集速率，且常因内存限制无法完成处理。为解决上述挑战，我们推出PetaKit5D——一款面向拍字节级光片图像高效处理的可扩展软件解决方案。该软件集成了一系列经过内存与性能优化的通用图像处理工具，其核心优势包括高速图像读写模块、快速且内存高效的几何变换、高性能Richardson-Lucy反卷积（Richardson-Lucy deconvolution）以及基于Zarr的可扩展拼接技术。这些特性较当前最优方法性能提升一个数量级以上，可实现全量太字节级体素规模的拍字节级图像数据处理…… 光片、双光子及相衬图像通过自制光片显微镜、双光子显微镜与斜射照明‘相衬’显微镜采集；宽场与共聚焦图像则通过安道尔（Andor）BC43台式共聚焦显微镜（牛津仪器公司，Oxford Instruments）采集。本数据集已通过PetaKit5D（https://github.com/abcucberkeley/PetaKit5D）处理。 # 题为《用于拍字节级光片显微镜数据的图像处理工具（第1/2部分）》的数据 --- 本图像数据为论文《用于拍字节级光片显微镜数据的图像处理工具》（[https://doi.org/10.1101/2023.12.31.573734](https://doi.org/10.1101/2023.12.31.573734)）的配图数据集： ## 数据与文件结构说明 ### 数据归档结构 20211003_Aang_largeFOV_11h_stepAndSettle.zip ├── 20211003_Aang_largeFOV_11h_stepAndSettle │ ├── flatfieldCorrection │ │ ├── averaged │ │ │ ├── 488.tif │ │ │ └── 560.tif │ ├── PSF │ │ ├── 488_NA0p4_sig0p1_highSN.tif │ │ └── 560_NA0p4_sig0p1_highSN.tif │ └── run01 │ ├── ImageList_run01.csv │ ├── Scan_Iter_0000_000*_000x_00*y_000z_000*t_Settings.txt │ ├── Scan_Iter_0000_000*_CamA_ch0_CAM1_stack0000_488nm_0000000msec_0155431219msecAbs_000x_00*y_000z_000*t.tif │ └── Scan_Iter_0000_000*_CamB_ch0_CAM1_stack0000_488nm_0000000msec_0155431219msecAbs_00...