baigouy / dat

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

1. Install python 3.7 or Anaconda 3.7 (if not already present on your system)

2. In a command prompt type:

   pip install --user --upgrade dendritic-arborization-tracer
   

   or

   pip3 install --user --upgrade dendritic-arborization-tracer
   

   NB:

   • 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'

3. To open the graphical user interface, type the following in a command:

   python -m dendritic_arborization_tracer
   

   or

   python3 -m dendritic_arborization_tracer