DOI: 10.5061/dryad.7j12m
title: Data from: Automated deep-phenotyping of the vertebrate brain

description: Here we describe an automated platform suitable for large-scale
 deep-phenotyping of zebrafish mutant lines, which uses optical projection
 tomography to rapidly image brain-specific gene expression patterns in 3D
 at cellular resolution. Registration algorithms and correlation analysis
 are then used to compare 3D expression patterns, to automatically detect
 all statistically significant alterations in mutants, and to map them onto
 a brain atlas. Automated deep-phenotyping of a mutation in the master
 transcriptional regulator fezf2 not only detects all known phenotypes but
 also uncovers important novel neural deficits that were overlooked in
 previous studies. In the telencephalon, we show for the first time that
 fezf2 mutant zebrafish have significant patterning deficits, particularly
 in glutamatergic populations. Our findings reveal unexpected parallels
 between fezf2 function in zebrafish and mice, where mutations cause
 deficits in glutamatergic neurons of the telencephalon-derived neocortex.
description: Source code 1: 3D
 anatomical brain atlasesThis RAR archive
 contains 3D brain atlases for 2 and 3 dpf embryos.OPT_InSitu_Atlas.rarSource code 2: Test datasets for OPT reconstruction and registration (part 1)These RAR archive files contain the following: (1) acquisition data from our OPT platform of a 2 dpf fezf2 mutant embryo stained with an in situ probe for ascl1a (folder 'data\OPT', extension '.mat'). This file serves as a test dataset for our OPT reconstruction source code. (2) Unstained reference fish (URFs; folder 'data\Registration\ referenceFish') and OPT reconstructions from 8 wild-type embryos (folder 'data\Registration\TestData_th_2dpf\wt') and 8 fezf2 mutant embryos (folder 'data\Registration\TestData_th_2dpf\mt') stained with an in situ probe for tyrosine hydroxylase (th). URFs for 2 dpf and 3 dpf are provided. All th-stained embryos are 2 dpf. These images serve as a test dataset for our registration source code. Source code for both OPT reconstruction and registration is available at https://github.com/aallalou/OPT-InSitu-Toolbox. Download all RAR archive files (parts 1 through 7) prior to extraction.data_OPT-InSitu-Toolbox.part1.rarSource code 2: Test datasets for OPT reconstruction and registration (part 2)These RAR archive files contain the following: (1) acquisition data from our OPT platform of a 2 dpf fezf2 mutant embryo stained with an in situ probe for ascl1a (folder 'data\OPT', extension '.mat'). This file serves as a test dataset for our OPT reconstruction source code. (2) Unstained reference fish (URFs; folder 'data\Registration\ referenceFish') and OPT reconstructions from 8 wild-type embryos (folder 'data\Registration\TestData_th_2dpf\wt') and 8 fezf2 mutant embryos (folder 'data\Registration\TestData_th_2dpf\mt') stained with an in situ probe for tyrosine hydroxylase (th). URFs for 2 dpf and 3 dpf are provided. All th-stained embryos are 2 dpf. These images serve as a test dataset for our registration source code. Source code for both OPT reconstruction and registration is available at https://github.com/aallalou/OPT-InSitu-Toolbox. Download all RAR archive files (parts 1 through 7) prior to extraction.data_OPT-InSitu-Toolbox.part2.rarSource code 2: Test datasets for OPT reconstruction and registration (part 3)These RAR archive files contain the following: (1) acquisition data from our OPT platform of a 2 dpf fezf2 mutant embryo stained with an in situ probe for ascl1a (folder 'data\OPT', extension '.mat'). This file serves as a test dataset for our OPT reconstruction source code. (2) Unstained reference fish (URFs; folder 'data\Registration\ referenceFish') and OPT reconstructions from 8 wild-type embryos (folder 'data\Registration\TestData_th_2dpf\wt') and 8 fezf2 mutant embryos (folder 'data\Registration\TestData_th_2dpf\mt') stained with an in situ probe for tyrosine hydroxylase (th). URFs for 2 dpf and 3 dpf are provided. All th-stained embryos are 2 dpf. These images serve as a test dataset for our registration source code. Source code for both OPT reconstruction and registration is available at https://github.com/aallalou/OPT-InSitu-Toolbox. Download all RAR archive files (parts 1 through 7) prior to extraction.data_OPT-InSitu-Toolbox.part3.rarSource code 2: Test datasets for OPT reconstruction and registration (part 4)These RAR archive files contain the following: (1) acquisition data from our OPT platform of a 2 dpf fezf2 mutant embryo stained with an in situ probe for ascl1a (folder 'data\OPT', extension '.mat'). This file serves as a test dataset for our OPT reconstruction source code. (2) Unstained reference fish (URFs; folder 'data\Registration\ referenceFish') and OPT reconstructions from 8 wild-type embryos (folder 'data\Registration\TestData_th_2dpf\wt') and 8 fezf2 mutant embryos (folder 'data\Registration\TestData_th_2dpf\mt') stained with an in situ probe for tyrosine hydroxylase (th). URFs for 2 dpf and 3 dpf are provided. All th-stained embryos are 2 dpf. These images serve as a test dataset for our registration source code. Source code for both OPT reconstruction and registration is available at https://github.com/aallalou/OPT-InSitu-Toolbox (Allalou, 2017). Download all RAR archive files (parts 1 through 7) prior to extraction.data_OPT-InSitu-Toolbox.part4.rarSource code 2: Test datasets for OPT reconstruction and registration (part 5)These RAR archive files contain the following: (1) acquisition data from our OPT platform of a 2 dpf fezf2 mutant embryo stained with an in situ probe for ascl1a (folder 'data\OPT', extension '.mat'). This file serves as a test dataset for our OPT reconstruction source code. (2) Unstained reference fish (URFs; folder 'data\Registration\ referenceFish') and OPT reconstructions from 8 wild-type embryos (folder 'data\Registration\TestData_th_2dpf\wt') and 8 fezf2 mutant embryos (folder 'data\Registration\TestData_th_2dpf\mt') stained with an in situ probe for tyrosine hydroxylase (th). URFs for 2 dpf and 3 dpf are provided. All th-stained embryos are 2 dpf. These images serve as a test dataset for our registration source code. Source code for both OPT reconstruction and registration is available at https://github.com/aallalou/OPT-InSitu-Toolbox (Allalou, 2017). Download all RAR archive files (parts 1 through 7) prior to extraction.data_OPT-InSitu-Toolbox.part5.rarSource code 2: Test datasets for OPT reconstruction and registration (part 6)These RAR archive files contain the following: (1) acquisition data from our OPT platform of a 2 dpf fezf2 mutant embryo stained with an in situ probe for ascl1a (folder 'data\OPT', extension '.mat'). This file serves as a test dataset for our OPT reconstruction source code. (2) Unstained reference fish (URFs; folder 'data\Registration\ referenceFish') and OPT reconstructions from 8 wild-type embryos (folder 'data\Registration\TestData_th_2dpf\wt') and 8 fezf2 mutant embryos (folder 'data\Registration\TestData_th_2dpf\mt') stained with an in situ probe for tyrosine hydroxylase (th). URFs for 2 dpf and 3 dpf are provided. All th-stained embryos are 2 dpf. These images serve as a test dataset for our registration source code. Source code for both OPT reconstruction and registration is available at https://github.com/aallalou/OPT-InSitu-Toolbox (Allalou, 2017). Download all RAR archive files (parts 1 through 7) prior to extraction.data_OPT-InSitu-Toolbox.part6.rarSource code 2: Test datasets for OPT reconstruction and registration (part 7)These RAR archive files contain the following: (1) acquisition data from our OPT platform of a 2 dpf fezf2 mutant embryo stained with an in situ probe for ascl1a (folder 'data\OPT', extension '.mat'). This file serves as a test dataset for our OPT reconstruction source code. (2) Unstained reference fish (URFs; folder 'data\Registration\ referenceFish') and OPT reconstructions from 8 wild-type embryos (folder 'data\Registration\TestData_th_2dpf\wt') and 8 fezf2 mutant embryos (folder 'data\Registration\TestData_th_2dpf\mt') stained with an in situ probe for tyrosine hydroxylase (th). URFs for 2 dpf and 3 dpf are provided. All th-stained embryos are 2 dpf. These images serve as a test dataset for our registration source code. Source code for both OPT reconstruction and registration is available at https://github.com/aallalou/OPT-InSitu-Toolbox (Allalou, 2017). Download all RAR archive files (parts 1 through 7) prior to extraction.data_OPT-InSitu-Toolbox.part7.rar