Glia removal

All scripts used for the analysis of the neuron segmentation are located in SyConn/scripts/multiviews_glia/.

Prerequisites

  • Knossos- and SegmentationDataset of the supervoxel segmentation

  • Initial RAG/SV-mapping

Steps

In order to generate the SSV multi-views prior to glia removal it is necessary to provide the script with an initial RAG/SV-mapping. The agglomerated SVs are required to provide sufficient context for the glia prediction: 
start_sso_rendering_glia_removal.py

In order to start the glia prediction run:

glia_prediction.py

SVs with predicted glia labels will be removed via a splitting heuristic. For splitting and generating the glia-free region adjacency graph (RAG) run:

glia_splitting.py

Preparing neuron analysis

Now create a new SSD, the post-glia-removal SSD, from the resulting RAG and run a dataset analysis to assign cell objects (mitochondria, vesicle clouds and synaptic junctions) to all its SSVs (see SSD).