status: experimental Cluster neurons based on synapse connections.

This application has numerous strategies for extracting features for different neurons that can be used for automatic clustering. These tools, for now, are intended to run within a Jupyter notebook and to enable users to find new neuron clusters or to evaluate previously create ones. It is also hoped that interactive exploration will aid the in creation of even better features.

Install conda.

% conda create -n typecluster
% conda install scipy scikit-learn umap-learn jupyter hvplot bokeh plotly neuprint-python pyarrow -n typecluster -c conda-forge -c flyem-forge
% source activate typecluster
% git clone https://github.com/connectome-neuprint/typecluster.git
% cd typecluster; python setup.py install
% export NEUPRINT_APPLICATION_CREDENTIALS=YOURTOKEN
% jupyter notebook 

To use the library, import typecluster.

• add more visualization widgets (especially to debug cluster features and to evalaute ground truth)
• create recipes for example workflows
• add example notebooks
• add functions for outlier analysis
• improve featues creation algorithms (e.g., iterative feature generation)
• create batch-based workflow to run with minimal supervision