Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
Ding, Yifu, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Vanselow, Daniel J, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Yakovlev, Maksim A, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Katz, Spencer R, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Lin, Alex Y, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Clark, Darin P, Duke University
Vargas, Phillip, University of Chicago
Xin, Xuying, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Copper, Jean E, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Canfield, Victor A, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Ang, Khai C, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Wang, Yuxin, OmniVision Technologies (United States)
Xiao, Xianghui, Brookhaven National Laboratory
Carlo, Francesco De, Argonne National Laboratory
Rossum, Damian B van, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Riviere, Patrick La, University of Chicago
Cheng, Keith, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, United States
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Using micro-CT optimized for cellular characterization (histo-tomography), brain nuclei can be computationally segmented and assigned to brain regions. Shape and volume can be computed for populations of nuclei, motor neurons and red blood cells. Computed cell density revealed striking individual phenotypic variation. Unlike histology, histo-tomography allows the detection of phenotypes that require millimeter scale context in multiple planes. We expect the computational and visual insights into 3D tissue architecture provided by histo-tomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
ReadMe
General instructions and information concerning files included herein.
33 dpf microCT reconstruction of juvenile zebrafish
33 dpf microCT reconstruction of juvenile zebrafish with nominal 1.43um voxel resolution. This is an 8-bit multi-page tiff series z-stack. We recommend opening with Fiji (Fiji Is Just ImageJ).
33dpf_1_sagittal_8bit_reconstruction_fig5_tiff_chenglab.7z
5 dpf (samples 1-5) microCT reconstructions of larval zebrafish
5, 5 dpf microCT reconstructions of larvalzebrafish with nominal .743um voxel resolution. These are 8-bit multi-page tiff series z-stacks. We recommend opening with Fiji (Fiji Is Just ImageJ) using the bio-formats plugin.
5dpf_1-5_axial_8bit_reconstructions_fig6,8_tiffs_chenglab.7z
Zebrafish Brain Segmentation and Nuclear Detection (Virtual Reality)
Virtual Reality project of our cell detection pipeline, viewable for free in the scientific VR platform syGlass View available here: https://www.syglass.io/view
Zebrafish_Brain_Segmentation_and_Nuclear_Detection.syg
Zebrafish Embryonic to Juvenile Development (Virtual Reality)
Virtual Reality project of a 2, 3, 4, 5 and 33 dpf zebrafish reconstructed with microCT, viewable for free in the scientific VR platform syGlass View available here: https://www.syglass.io/view
Zebrafish_Embryonic_to_Juvenile_Development.syg
Zebrafish Juvenile 1.43um voxel size (Virtual Reality)
Virtual Reality project of a 33 dpf juvenile zebrafish reconstructed with microCT, viewable for free in the scientific VR platform syGlass View available here: https://www.syglass.io/view
Zebrafish_Juvenile_1.43um_voxel_size.syg
Registration Pipeline
Files are provided for registering our manually segmented 5-dpf fish onto our other samples. Uses elastix/transformix, which can be found here: http://elastix.isi.uu.nl/
registration_pipeline_fig6_chenglab.7z
Nuclear Detection Validation
Validation of our nuclear detection pipeline is provided, scripts and user segmentations are provided herein.
validation_fig7,7s1_chenglab.7z
Nuclei positioning and characteristics
Nuclei position and morphological characteristics provided by simpleITK analysis are provided herein as .csv files.
simpleITK_nuclear_detection_chenglab.7z
Nuclear detection probabilities 5 dpf (samples 1-5)
Nuclear detection probabilities of each 5 dpf sample analyzed provided as individual 32-bit multi-page tiff z-stacks. We recommend opening in Fiji (Fiji Is Just ImageJ).
5dpf_1-5_axial_32bit_nuclear_detection_probabilities_fig7,7s1_tiff_chenglab.7z
5 dpf (samples 1-5) anatomical brain region segmentations
Segmentations of anatomical brain regions in the same space as nuclear detections are provided herein.
5dpf_1-5_axial_8bit_brain_region_segmentations_fig7,8,9_tiffs_chenglab.7z