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A tool to segment dendrites

Project description

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
    

Project details


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This version

0.1

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