The Neuron Analyzer 2D application offers advanced functionality to analyze 2D fluorescence microscope images of neurons.
neuron boundary detection based on active contours
identification of structural neuron parts, like soma, neurites, growth cones
morphology analysis, e.g., neurite length, average neurite width, number of branch and end points, growth cone size and shape roundness, ...
optional: extraction of molecular profiles from the given molecules, like labeled proteins, along the neurites from soma to growth cones
optional: detection of molecular particles, for example FISH data, along the neurites from soma to growth cones
intermediate and final results are automatically saved
tabular presentation of result data
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The output directory is created within the image input directory
Image of detected neurites are saved in the result directory
Table of measuerements, obtained from the detection results
Profiles of protein distributions are saved in the result directory (optional)
Image of detected particles along the detected neurites (optional)
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Neurite Detector
Detector to use for neurite detection
Configurable via GUI (see Neurite Detector 2D)
Extract Profiles
Option to choose molecular profile extraction
default: true
Define Molecules
Molecule names of each image channel
used if Extract Profiles is set to true
default: Tubulin, ZBP, Actin, DAPI
Profile Molecule Channels
Channels of fluorescence stains to use for molecular profile extraction
used if Extract Profiles is set to true
default: 1,2,3
Extract Particles
Option to choose molecular particle extraction, e.g. FISH data
default: false
Particle Detector
Detector to use for particle detection
Configurable via GUI (see Neurite Particle Detector 2D)
used if Extract Particles is set to true
Verbose
Output of additional messages on console is disabled/enabled
default: false