This dataset accompanies the article of the same title in the journal Plos Biology. It includes a) Ground truth datasets for the training of the StarDist neuronal network for nucleus segmentation (StardistTraining.tar.gz) b) The trained Stardist nucleus segmentation model (StardistModel.tar.gz c) raw and segmented data for the training of the cell type classification (CelltypeClassification.tar.gz, CelltypeClassificationExcInhNeurons.tar.gz) d) the raw and segmented data for the results of the paper (RawdataResults.tar.gz) e) Ground truth data for the training of all classifiers (ClassificationTrainingDataSet.tab)