Dendritic spines are the seat of most excitatory synapses in the brain, and a cellular structure considered central to learning, memory, and activity-dependent plasticity. The quantification of dendritic spines from light microscopy data is usually performed by humans in a painstaking and error-prone process. We found that human-to-human variability is substantial (inter-rater reliability 82.2±6.4 %), raising concerns about the reproducibility of experiments and the validity of using human-annotated 'ground truth' as an evaluation method for computational approaches of spine identification. To address this, we present DeepD3, an open deep learning-based framework to robustly quantify dendritic spines in microscopy data in a fully automated fashion. DeepD3's neural networks have been trained on data from different sources and experimental conditions, annotated and segmented by multiple experts and they offer precise quantification of dendrites and dendritic spines. Importantly, these networks were validated in a number of datasets on varying acquisition modalities, species, anatomical locations and fluorescent indicators. The entire DeepD3 open framework, including the fully segmented training data, a benchmark that multiple experts have annotated, and the DeepD3 model zoo is fully available, addressing the lack of openly available datasets of dendritic spines while offering a ready-to-use, flexible, transparent, and reproducible spine quantification method.
DeepD3 is installable using
pip install deepd3,
see the Code section for further instructions.
The most convenient way is to use our graphical user interface (GUI)
to open your data and process it using our pipeline. Pre-trained
deep neural networks for dendritic spines and dendrite segmentation
can be found in our Model Zoo.
If you trained your network with a fixed shape (e.g. 128x128x1), you can use this script/Jupyter notebook to convert your network to a generic one.
We provide openly our pre-trained model zoo on Zenodo and on our respective Model Zoo section here. If you would like to contribute your custom model, please use the following form to submit your model.