Data from: Automated deep-phenotyping of the vertebrate brain

Allalou A, Wu Y, Ghannad-Rezaie M, Eimon PM, Yanik MF

Date Published: April 21, 2017

DOI: http://dx.doi.org/10.5061/dryad.7j12m

 

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Title Source code 1: 3D anatomical brain atlases
Downloaded 29 times
Description This RAR archive contains 3D brain atlases for 2 and 3 dpf embryos.
Download OPT_InSitu_Atlas.rar (988.6 Mb)
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Title Source code 2: Test datasets for OPT reconstruction and registration (part 1)
Downloaded 24 times
Description 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.
Download data_OPT-InSitu-Toolbox.part1.rar (943.7 Mb)
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Title Source code 2: Test datasets for OPT reconstruction and registration (part 2)
Downloaded 28 times
Description 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.
Download data_OPT-InSitu-Toolbox.part2.rar (943.7 Mb)
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Title Source code 2: Test datasets for OPT reconstruction and registration (part 3)
Downloaded 25 times
Description 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.
Download data_OPT-InSitu-Toolbox.part3.rar (943.7 Mb)
Details View File Details
Title Source code 2: Test datasets for OPT reconstruction and registration (part 4)
Downloaded 26 times
Description 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.
Download data_OPT-InSitu-Toolbox.part4.rar (943.7 Mb)
Details View File Details
Title Source code 2: Test datasets for OPT reconstruction and registration (part 5)
Downloaded 22 times
Description 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.
Download data_OPT-InSitu-Toolbox.part5.rar (943.7 Mb)
Details View File Details
Title Source code 2: Test datasets for OPT reconstruction and registration (part 6)
Downloaded 20 times
Description 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.
Download data_OPT-InSitu-Toolbox.part6.rar (943.7 Mb)
Details View File Details
Title Source code 2: Test datasets for OPT reconstruction and registration (part 7)
Downloaded 23 times
Description 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.
Download data_OPT-InSitu-Toolbox.part7.rar (653.9 Mb)
Details View File Details

When using this data, please cite the original publication:

Allalou A, Wu Y, Ghannad-Rezaie M, Eimon PM, Yanik MF (2017) Automated deep-phenotyping of the vertebrate brain. eLife 6: e23379. http://dx.doi.org/10.7554/eLife.23379

Additionally, please cite the Dryad data package:

Allalou A, Wu Y, Ghannad-Rezaie M, Eimon PM, Yanik MF (2017) Data from: Automated deep-phenotyping of the vertebrate brain. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7j12m
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