Simple Neurite Tracer: Accurate point placement

Revision as of 14:37, 21 August 2015 by Rueden (talk | contribs) (Use arrow template for menu commands)

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Note that there were recent changes that made the use of the plugin in three pane mode much easier, so make sure that you have an up-to-date Fiji by running "Help › Update Fiji".


Sometimes people have reported problems with placing points accurately. Many of these issues can be resolved just by placing the points when:

  • Using the "Three pane view"
  • Zoomed in to 600% or so

A step by step guide is given below:


When starting up, make sure that "Three pane view" is turned on:

Simple Neurite Tracer Accurate point placement-1.png

Find the approximate location of your start point by moving your mouse in the XY window, holding down Shift to synchronize the view in the other panes:

Simple Neurite Tracer Accurate point placement-2.png

When you press + to zoom in, all the panes will zoom in on the point that the crosshairs is over, so each time you press +, make sure you move your mouse pointer so that it's still over the structure of interest:

Simple Neurite Tracer Accurate point placement-3.png

To make sure you're clicking in the centre of the structure, try moving the mouse and scroll wheel in each of the panes (holding down Shift so synchronize the views in all three panes). When you're happy with the point under the crosshairs, click to start the path:

Simple Neurite Tracer Accurate point placement-4.png

Zoom out again with the - key, and similarly zoom in on the next point you want to be on your path to place it precisely:

Simple Neurite Tracer Accurate point placement-5.png

The path along the neuron may not follow the centre line:

Simple Neurite Tracer Accurate point placement-6.png

... but you can later improve that with the "Fit Volume" option, which tries to fix the midline and radius to sub-voxel accuracy:

Simple Neurite Tracer Accurate point placement-7.png