2026-06-03T10:32:02Zhttps://www.radar-service.eu/oai/OAIHandler10.48606/152026-04-24T07:43:19Z
10.48606/15
Capek, Daniel
Daniel
Capek
0000-0001-5199-9940
University of Konstanz
Kurzbach, Anica
Anica
Kurzbach
0000-0003-1531-3088
Universität Konstanz
Safroshkin, Matvey
Matvey
Safroshkin
0000-0003-3955-5081
Computer Vision Studio Tübingen
Morales-Navarrete, Hernan
Hernan
Morales-Navarrete
0000-0002-9578-2556
Universität Konstanz
Arutyunov, Grigory
Grigory
Arutyunov
0000-0002-4372-9155
Computer Vision Studio Tübingen
Toulany, Nikan
Nikan
Toulany
0000-0003-3505-7325
Universität Konstanz
Datasets for "EmbryoNet: Using deep learning to link embryonic phenotypes to signaling pathways"
Universität Konstanz
2022
2022
Biology
machine learning, phenotypes, cell signaling, development, phenomic screen, high-throughput, zebrafish, medaka, stickleback
Overview of the EmbryoNet datapackages
Open Access
Creative Commons Attribution 4.0 International
Müller, Patrick
Bihler, Johanna
Friedrich-Miescher-Labor der Max-Planck-Gesellschaft
Jordan, Ben
Sense AI, Minneapolis
Hagauer, Julia
Friedrich-Miescher-Labor der Max-Planck-Gesellschaft
Kick, Sebastian
Friedrich-Miescher-Labor der Max-Planck-Gesellschaft
Jones, Felicity
0000-0002-5027-1031
Friedrich-Miescher-Labor der Max-Planck-Gesellschaft
Müller, Patrick
0000-0002-0702-6209
Universität Konstanz
This is the data repository of the training and test data sets for EmbryoNet. The data is structured in multiple packages. EmbryoNet_Models (DOI 10.48606/31) contains the trained neural networks, the other packages are imaging data. All data are brightfield timelapse images of one or multiple embryos recorded in multiwell plates in either the Acquifer Imaging Machine or the Keyence BZ-X810 microscope. The microscope type is included in the name of the archive, e.g. BMP_Acquifer.zip. Training data images are accompanied by json-files with the classification from human annotators, while test data sets also have the jsons of EmbryoNet's classification. The dataset EmbryoNet_Image-data: Stickleback 1 (DOI 10.48606/32) contains training data for the Stickleback version of EmbryoNet, and EmbryoNet_Test-data: Stickleback (DOI 10.48606/33) contains the evaluation data. EmbryoNet_Training-data: Medaka (DOI 10.48606/35) and EmbryoNet_Test-data: Medaka (DOI 10.48606/34) contain the respective data for Medaka. The other packages are zebrafish images. The two archives named EmbryoNet_Test-data 1&2 (DOI: 10.48606/29 & 10.48606/30) are the zebrafish test data sets. The zebrafish training data sets are named after the signaling molecule: EmbryoNet_training-data: BMP (DOI 10.48606/18), EmbryoNet_training-data: Retinoic acid (DOI 10.48606/20), EmbryoNet_training-data: Wnt (DOI 10.48606/21), EmbryoNet_training-data: FGF (DOI 10.48606/22), EmbryoNet_training-data: Nodal (DOI 10.48606/23), EmbryoNet_training-data: Shh (DOI 10.48606/25) and EmbryoNet_training-data: PCP (DOI 10.48606/26). EmbryoNet_training-data: WT (DOI 10.48606/16) contains the training data of untreated embryos. The datasets EmbryoNet_Training-data: Severities - Keyence (DOI 10.48606/28) and EmbryoNet_Training-data: Severities - Acquifer (DOI 10.48606/27) contain the training and evaluation data of the Severities experiments with different inhibitor concentrations. Inside a zip file the data is arranged in experiment folders, named in the format DATE_Molecule_concentration, e.g. 201222_FGF_10uM. Inside these experiment folders the data is organized after multiwell plate or microscope positions, A001-D006 for the Acquifer data and XY01-XY24 for the Keyence data.
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