Neuron Tracer

A head start on hand tracing, for the NeuronJ plugin for Fiji.

Upload an image of a sensory neuron and this will attempt to trace it and gather statistics on the result. You get back an NDF file you can open in NeuronJ to continue where the tracer left off, plus JPEGs that show what it found.

Images are traced in memory and thrown away as soon as the result is sent back. Nothing is stored on the server.

How to use it

  1. For best results, fill in the cell body with a pink color. Otherwise the tracer will try to detect it automatically, but if it is not dark enough the results may vary.
  2. Choose a sensory neuron image. See the examples further down the page.
  3. Adjust the tuning values if you need to, then press Trace image.
  4. Check the preview to see how the trace turned out.
  5. Download the archive to get the traced images and the NDF file.

Trace an image

No file chosen yet.

Higher values look at lighter pixels, but may be less accurate.

Raise this if branches leaving the cell body are being missed.

How far from the cell body the search for starting branches begins.

Result

Upload an image to get started.

Examples

A high contrast image where the cell body is the same shade as the branches needs the cell body filled in with pink first.

High contrast neuron with the cell body filled in pink
A high contrast image with the cell body filled in.
Original neuron image before any edits
1. The original image.
The same neuron with its cell body filled in pink
2. Cell body filled in pink.
Traced branches drawn over the original image
3. Branches traced over the original.
Traced branches drawn on a white background
4. The same trace on white.