10.5061/DRYAD.4NB12G2
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
Data from: Computational 3D histological phenotyping of whole zebrafish by
X-ray histotomography
Dryad
dataset
2019
whole-organism phenomics
3D Imaging
Volumetric histology
phenotypic variation
Danio rerio
registration
Micro-CT
Virtual reality
2019-06-12T14:49:56Z
2019-06-12T14:49:56Z
en
https://doi.org/10.7554/elife.44898
25574751073 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
ReadMeGeneral instructions and information concerning files included
herein.33 dpf microCT reconstruction of juvenile zebrafish33 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.7z5 dpf
(samples 1-5) microCT reconstructions of larval zebrafish5, 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.7zZebrafish 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/viewZebrafish_Brain_Segmentation_and_Nuclear_Detection.sygZebrafish 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/viewZebrafish_Embryonic_to_Juvenile_Development.sygZebrafish 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/viewZebrafish_Juvenile_1.43um_voxel_size.sygRegistration PipelineFiles 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.7zNuclear Detection ValidationValidation of our nuclear detection pipeline is provided, scripts and user segmentations are provided herein.validation_fig7,7s1_chenglab.7zNuclei positioning and characteristicsNuclei position and morphological characteristics provided by simpleITK analysis are provided herein as .csv files.simpleITK_nuclear_detection_chenglab.7zNuclear 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.7z5 dpf (samples 1-5) anatomical brain region segmentationsSegmentations 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