Datasets for "EmbryoNet: Using deep learning to link embryonic phenotypes to signaling pathways"

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.