Dendritic Arborization Tracer
Dendritic Arborization Tracer is a tool to segment neurons along with their dendrites. Ideally, it takes a single channel image as input.
- The neuron mask is detected in the 'Mask neuron' tab
- The cell body mask is detected in the 'Mask cell body' tab
- Finally, the neuron is skeletonized in the 'Segment dendrites' tab using skeletonization or using the watershed algotrithm. Once skeletonized, the neuron can be further segmented to identify dendrites.
Install
-
Install python 3.7 or Anaconda 3.7 (if not already present on your system)
-
In a command prompt type:
pip install --user --upgrade dendritic-arborization-traceror
pip3 install --user --upgrade dendritic-arborization-tracerNB:
- To open a command prompt on Windows press 'Windows'+R then type 'cmd'
- To open a command prompt on MacOS press 'Command'+Space then type in 'Terminal'
-
To open the graphical user interface, type the following in a command:
python -m dendritic_arborization_traceror
python3 -m dendritic_arborization_tracer
1 maintainer
Metadata
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Release files for dendritic-arborization-tracer 0.1
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