Neuronal morphology analysis and classification

All scripts used for the analysis of the neuron segmentation are located in SyConn/scripts/multiviews_neuron/, namely:

  • SSV multi-views generation: start_sso_rendering.py

  • Cell compartment prediction: axoness_prediction.py and spiness_prediction.py

  • Cell type prediction: celltype_prediction.py

Prerequisites

  • Knossos- and SegmentationDataset of the supervoxel segmentation

  • SegmentationDatasets for all cellular organelles (currently mitochondria, vesicle clouds and synaptic junctions)

  • [Optional] Glia removal

  • The RAG/SV-mapping in form of a SSD, see SuperSegmentationDatasets

  • Mapped cellular organelles to SSVs

Steps

The multi-views contain shape information of cellular organelles and the cell/SSV outline and are the basis for predicting cell compartments, cell type and spines. To generate them dataset-wide run: 
start_sso_rendering.py

Dataset-wide predictions can be started via the respective scripts:

  • Cell compartments: axoness_prediction.py and spiness_prediction.py

  • Cell types: celltype_prediction.py

Their results are stored on SSV level and used for extracting the wiring diagram later on.