Difference between revisions of "Simple Neurite Tracer: Accurate point placement"

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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".
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#REDIRECT [[SNT:_Step-By-Step_Instructions#Accurate_Point_Placement]]
 
 
=== 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:
 
 
 
[[Image: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:
 
 
 
[[Image: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:
 
 
 
[[Image:Simple_Neurite_Tracer_Accurate_point_placement-3.png]]
 
 
 
Then click to start the path:
 
 
 
[[Image: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:
 
 
 
[[Image:Simple_Neurite_Tracer_Accurate_point_placement-5.png|750px]]
 
 
 
The path along the neuron may not follow the centre line:
 
 
 
[[Image:Simple_Neurite_Tracer_Accurate_point_placement-6.png|750px]]
 
 
 
... but you can later improve that with the "Fit Volume" option, which tries to fix the midline and radius to sub-voxel accuracy:
 
 
 
[[Image:Simple_Neurite_Tracer_Accurate_point_placement-7.png]]
 
 
 
[[Category:Tutorials]]
 

Latest revision as of 22:12, 18 May 2019