DSM: Deep Sequential Model for Complete Neuronal Morphology Representation and Feature Extraction

This is an open-source repository for hosting codes and data files from research, "DSM: Deep Sequential Model for Complete Neuronal Morphology Representation and Feature Extraction". We also provided a web service based on our methods, please go to http://101.43.104.173:8501/. (1)raw_dataset.zip: 1,282 neuron reconstructions from SEU-Allen dataset; 1,002 neuron reconstructions from Janelia dataset; 1,100 neuron reconstructions from ION dataset. (2)Supplementary.zip: Supplementary information, including tables and figures; (3)DSM-tools.zip: A python package for converting neuron morphology into sequences and implementing DSM models. NeuronSequenceDataset class: to transform SWC files to sequence dataframes by binary tree traversals, and prepare for the input of DSM networks. DSMDataConverter class: a helper to convert the sequence dataframes for classification and clustering. DSMHierarchicalAttentionNetwork class: classification model, giving a pre-trained DSM-HAN model by default. DSMAutoencoder class: clustering model, giving a pre-trained DSM-AE model by default. (4)neuron2seq_for_developer.zip: A repository for further development of the models, including source codes and all data files.