🧠 Cochlear Neurofilament Tracer

Trace auditory-nerve fibers in confocal z-stacks and quantify them per frequency region, separating IHC-innervating from OHC-innervating fibers using the Myo7a hair-cell channel.

Channels expected: Neurofilament (traces the neuron) and Myo7a (hair cells — reference to split IHC vs OHC). IHCs form a single row, OHCs form three rows, so the Myo7a band is used to place the IHC/OHC boundary — which you can fine-tune by hand.

Input: Zeiss .czi z-stacks or generic .tif/.tiff stacks.

Upload CZI or TIFF

Neurofilament channel

Myo7a channel

Frequency region

IHC / OHC region split (Myo7a-guided)

Split axis (Y = radial, usual)

Y X

Which side is IHC?

Low side = IHC High side = IHC

Boundary position (fraction along split axis)

0 1

Tracing

Sensitivity (↑ = capture more/thinner fibers)

0.5 1.5

Min fiber length to count (µm)

0 20

Neurofilament (MIP)

Myo7a (MIP) + boundary

Traced neurons — white on black

Region overlay (cyan = IHC, magenta = OHC)

Quantification

Downloads (skeleton PNG + Excel)

Method: the Neurofilament channel is smoothed, thresholded (Otsu, scaled by the sensitivity control) and skeletonised in 3D; length, diameter (from the 3D distance transform), branch points and footprint area are measured with physical voxel spacing. Each fiber is a connected skeleton component ≥ the minimum length. The Myo7a band defines the IHC/OHC boundary, and metrics are reported for each region.