Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Ding Y, Vanselow DJ, Yakovlev MA, Katz SR, Lin AY, Clark DP, Vargas P, Xin X, Copper JE, Canfield VA, Ang KC, Wang Y, Xiao X, Carlo FD, Rossum DBv, Riviere PL, Cheng K

Date Published: June 12, 2019

DOI: https://doi.org/10.5061/dryad.4nb12g2.2

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Title ReadMe
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Description General instructions and information concerning files included herein.
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Title 33 dpf microCT reconstruction of juvenile zebrafish
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Description 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).
Download 33dpf_1_sagittal_8bit_reconstruction_fig5_...ab.7z (2.080 Gb)
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Title 5 dpf (samples 1-5) microCT reconstructions of larval zebrafish
Description 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.
Download 5dpf_1-5_axial_8bit_reconstructions_fig6,8...ab.7z (4.968 Gb)
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Title Zebrafish Brain Segmentation and Nuclear Detection (Virtual Reality)
Description 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
Download Zebrafish_Brain_Segmentation_and_Nuclear_...on.syg (741.8 Mb)
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Title Zebrafish Embryonic to Juvenile Development (Virtual Reality)
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Description 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
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Title Zebrafish Juvenile 1.43um voxel size (Virtual Reality)
Description 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
Download Zebrafish_Juvenile_1.43um_voxel_size.syg (3.213 Gb)
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Title Registration Pipeline
Description 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/
Download registration_pipeline_fig6_chenglab.7z (8.262 Gb)
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Title Nuclear Detection Validation
Description Validation of our nuclear detection pipeline is provided, scripts and user segmentations are provided herein.
Download validation_fig7,7s1_chenglab.7z (32.41 Mb)
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Title Nuclei positioning and characteristics
Description Nuclei position and morphological characteristics provided by simpleITK analysis are provided herein as .csv files.
Download simpleITK_nuclear_detection_chenglab.7z (19.53 Mb)
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Title Nuclear detection probabilities 5 dpf (samples 1-5)
Description 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).
Download 5dpf_1-5_axial_32bit_nuclear_detection_pro...ab.7z (2.268 Gb)
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Title 5 dpf (samples 1-5) anatomical brain region segmentations
Description Segmentations of anatomical brain regions in the same space as nuclear detections are provided herein.
Download 5dpf_1-5_axial_8bit_brain_region_segmentat...ab.7z (9.518 Mb)
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When using this data, please cite the original publication:

Ding Y, Vanselow DJ, Yakovlev MA, Katz SR, Lin AY, Clark DP, Vargas P, Xin X, Copper JE, Canfield VA, Ang KC, Wang Y, Xiao X, De Carlo F, van Rossum DB, La Riviere P, Cheng K (2019) Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography. eLife. https://doi.org/10.7554/elife.44898

Additionally, please cite the Dryad data package:

Ding Y, Vanselow DJ, Yakovlev MA, Katz SR, Lin AY, Clark DP, Vargas P, Xin X, Copper JE, Canfield VA, Ang KC, Wang Y, Xiao X, Carlo FD, Rossum DBv, Riviere PL, Cheng K (2019) Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography. Dryad Digital Repository. https://doi.org/10.5061/dryad.4nb12g2.2
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