Simple Neurite Tracer: Accurate point placement

Revision as of 08:15, 10 September 2010 by Mark (talk | contribs)

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".

Summary

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:

Step-by-step

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

Then 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

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