DOI: 10.5061/dryad.4nb12g2
title: Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

description: 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.
description: 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