DOI: 10.5061/dryad.kh18932g4
title: Data for: Image processing tools for petabyte-scale light sheet microscopy data (Part 1/2)

description: 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 rates of modern imaging cameras. The software opens new
 avenues for biological discoveries through large-scale imaging
 experiments.
description: 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).
description: # 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". Nature Methods (2024).
 [https://doi.org/10.1038/s41592-024-02475-4](https://doi.org/10.1038/s41592-024-02475-4). (bioRxiv, [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_000x_00*y_000z_000*t.tif 20220115_LLCPK_cell_data.zip ├── 20220115_LLCPK_cell_data │   ├── ImageList_from_encoder_timepoint_0.csv │   ├── Scan_Iter_0000_0000_000x_00*y_000z_0000t_JSONsettings.json │   ├── Scan_Iter_0000_0000_000x_00*y_000z_0000t_Settings.txt │   ├── Scan_Iter_0000_0000_000x_00*y_000z_0000t_TargetPositions.csv │   └── Scan_Iter_0000_0000_CamA_ch0_CAM1_stack0000_488nm_0000000msec_0106*msecAbs_000x_00*y_000z_0000t.tif 20220325_ISM_TPE_Mouse_Good_TPE_Structure_TPE_XYZ_Tile_AO.zip ├── 20220325_ISM_TPE_Mouse_Good_TPE_Structure_TPE_XYZ_Tile_AO │   ├── named │   │   ├── ImageList_ISM_from_encoder.csv │   │   ├── Scan_Iter_0000_CamA_ch0_CAM3_stack0000_920nm_0000000msec_000000*msecAbs_00*x_00*y_00*z_0000t.tif │   │   └── SliceList_Scan_Iter_0000_CamA_ch0_CAM3_stack0000_920nm_0000000msec_000000*msecAbs_00*x_00*y_00*z_0000t.tifpart0.csv │   └── PSF │   └── Cleaned__TPE_PSF_Mean_100nmXYZ.tif 20220427_Phase_Good_HeLa.zip ├── 20220427_Phase_Good_HeLa │   ├── ImageList_all_timepoints.csv │   └── Scan_Iter_000*_CamB_ch0_CAM1_stack0000_642nm_0000000000000msec_00000065*msecAbs_00*x_00*y_000z_000*t.tif 2024-05-16_Widefield_Confocal.zip ├── 2024-05-16_Widefield_Confocal │   ├── Confocal_raw.tif │   ├── PSFs │   │   ├── 2024-05-16_PSF_488_Beads_Confocal_test_PSF_1.tif │   │   └── 2024-05-16_PSF_488_Beads_WF_test_1_PSF_1.tif │   └── WF_raw.tif README.md ``` ### File Details This dataset contains the representative datasets for the the paper "Image processing tools for petabyte-scale light sheet microscopy data". Nature Methods (2024). [https://doi.org/10.1038/s41592-024-02475-4](https://doi.org/10.1038/s41592-024-02475-4). (bioRxiv, [https://doi.org/10.1101/2023.12.31.573734](https://doi.org/10.1101/2023.12.31.573734)) #### 20211003\_Aang\_largeFOV\_11h\_stepAndSettle (after decompressing the zip file): Long-term Large FOV Live Cell Imaging for LLC-PK1 Cells with Nuclei and Endoplasmic Reticulum (ER) Imaged with Lattice Light-Sheet Microscopy flatfieldCorrection: folder that contains flatfield images PSF: folder that contains PSF images run01: folder that contains the image data #### 20211003\_Aang\_largeFOV\_11h\_stepAndSettle/flatfieldCorrection: averaged: folder that contains flatfield images #### 20211003\_Aang\_largeFOV\_11h\_stepAndSettle/flatfieldCorrection/averaged: *.tif: flatfield images #### 20211003\_Aang\_largeFOV\_11h\_stepAndSettle/PSF: *.tif: PSF images #### 20211003\_Aang\_largeFOV\_11h\_stepAndSettle/run01: ImageList_run01.csv: csv file containing the image list *Settings.txt: txt file containing meta data Scan_Iter_0000_000*_Cam*_ch0_CAM1_stack0000_488nm_0000000msec_0155431219msecAbs_000x_00*y_000z_000*t.tif: tiled image data * Scan: image prefix * Iter_0000_000*: absolute timepoint (* is a number) * Cam*_ch0_CAM1: camera and channel (* is the letter A or B) * stack0000: stack number * 488nm: image laser wavelength (may not be exact) * 0000000msec_0155431219msecAbs: time stamps in milliseconds * 000x: x tile position * 00*y: y tile position (* is a number) * 000z: z tile position * 000*t: timepoint tile position (* is a number) #### 20220115\_LLCPK\_cell\_data (after decompressing the zip file): Large FOV Live Cell Imaging for LLC-PK1 Cells with Nuclei Imaged with Lattice Light-Sheet Microscopy ImageList_from_encoder_timepoint_0.csv: csv file containing the image list *JSONsettings.json: json file containing meta data *Settings.txt: txt file containing meta data *TargetPositions.csv: csv file containing target positions Scan_Iter_0000_0000_CamA_ch0_CAM1_stack0000_488nm_0000000msec_0106*msecAbs_000x_00*y_000z_0000t.tif: tiled image data * Scan: image prefix * Iter_0000_0000: absolute timepoint * CamA_ch0_CAM1: camera and channel * stack0000: stack number * 488nm: image laser wavelength (may not be exact) * 0000000msec_0106*msecAbs: time stamps in milliseconds (* is a number) * 000x: x tile position * 00*y: y tile position (* is a number) * 000z: z tile position * 0000t: timepoint tile position #### 20220325\_ISM\_TPE\_Mouse\_Good\_TPE\_Structure\_TPE\_XYZ\_Tile\_AO (after decompressing the zip file): Two-Photon Large FOV Live Imaging of Mouse Brain named: folder that contains the image data PSF: folder that contains PSF images #### 20220325\_ISM\_TPE\_Mouse\_Good\_TPE\_Structure\_TPE\_XYZ\_Tile\_AO/named: ImageList_ISM_from_encoder.csv: csv file containing the image list Scan_Iter_0000_CamA_ch0_CAM3_stack0000_920nm_0000000msec_000000*msecAbs_00*x_00*y_00*z_0000t.tif: tiled image data * Scan: image prefix * Iter_0000: absolute timepoint * CamA_ch0_CAM3: camera and channel * stack0000: stack number * 920nm: image laser wavelength (may not be exact) * 0000000msec_000000*msecAbs: time stamps in milliseconds (* is a number) * 00*x: x tile position (* is a number) * 00*y: y tile position (* is a number) * 00*z: z tile position (* is a number) * 0000t: timepoint tile position SliceList*.csv: csv file containing the slice list #### 20220325\_ISM\_TPE\_Mouse\_Good\_TPE\_Structure\_TPE\_XYZ\_Tile\_AO/PSF: Cleaned__TPE_PSF_Mean_100nmXYZ.tif: PSF image #### 20220427\_Phase\_Good\_HeLa (after decompressing the zip file): Oblique Illumination "Phase" Large FOV Imaging of HeLa Cells time series ImageList_all_timepoints.csv: csv file containing the image list Scan_Iter_000*_CamB_ch0_CAM1_stack0000_642nm_0000000000000msec_00000065*msecAbs_00*x_00*y_000z_000*t.tif: tiled image data * Scan: image prefix * Iter_000*: absolute timepoint (* is a number) * CamB_ch0_CAM1: camera and channel * stack0000: stack number * 642nm: image laser wavelength (may not be exact) * 0000000msec_00000065*msecAbs: time stamps in milliseconds (* is a number) * 00*x: x tile position (* is a number) * 00*y: y tile position (* is a number) * 000z: z tile position * 000*t: timepoint tile position (* is a number) #### 2024-05-16\_Widefield\_Confocal (after decompressing the zip file): 3D Widefield and Confocal Images of LLC-PK1 Cells Confocal_raw.tif: confocal image PSFs: folder that contains PSF images WF_raw.tif: widefield image #### 2024-05-16\_Widefield\_Confocal/PSFs: *.tif: PSF images ## Code/Software The data was processed with PetaKit5D ([https://github.com/abcucberkeley/PetaKit5D](https://github.com/abcucberkeley/PetaKit5D)).