The Neurite Detector 2D application offers advanced functionality to detect neurites in 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, ...
intermediate and final results are automatically saved
visual and tabular presentation of result data
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Image of detected neurites
Table of measuerements, obtained from the detection results
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Input Directory
Directory of input image(s)
Nuclei Channel
Channel number of the nuclei image channel
range [1, #ImageChannels]
default: 4
Neuron Channels
Channel numbers of all image channels that stain the neuron for detection
range [1, #ImageChannels]
default: 1,2,3
Maximum spine Length [pixel]
Maximum length to define a branch as spine (filopodia-like protrusion)
value >= 0
default: 53
Neurite Color
Color of the neurite regions in result image
Verbose
Output of additional messages on console is disabled/enabled
default: false
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Input Directory
Directory of input image(s)
Nuclei Channel
Channel number of the nuclei image channel
range [1, #ImageChannels]
default: 4
Neuron Channels
Channel numbers of all image channels that stain the neuron for detection
range [1, #ImageChannels]
default: 1,2,3
Maximum spine Length [pixel]
Maximum length to define a branch as spine (filopodia-like protrusion)
value >= 0
default: 53
Neurite Mask Size [pixel]
Maximum of average width of a neurite
value >= 0
default: 21
Maximum Fragment Distance [pixel]
Maximum neuron fragment distance
value >= 0
default: 50
Niblack Constant
..Niblack threshold contant
default: 0.8
Detector Mode
Mode of neurite detector
default: DETECTION
External Energy
External snake energy label
default: DISTANCE_MAP
Alpha
Weighting factor for snake length term
range [0.0, 1.0]
default: 0.2
Beta
Weighting factor for snake curvature term
range [0.0, 1.0]
default: 0.0
Step Size
Step size of snake movement
value >= 0.0
default: 0.05
Resample Constant
Snake point resampling constant
value > 0
default: 5
Motion Fraction [percent]
Minimum fraction of point motion to stop snake optimization
Optimization stops, if more then fraction percent of snake points are not moved within a iteration step
range [0.0, 1.0]
default: 0.95
Maximum Iterations
Maximum number of iteration steps
value >= 0.0
default: 120
Neurite Color
Color of the neurite regions in result image
Verbose
Output of additional messages on console is disabled/enabled
default: false