Help in measuring area with the 'wand'


Did you happen to save this macro so that I could access it. If so what did you name it. Thanks



How did you determine that either method was an over or under estimation of the area and not closer to the actual area?

I think this is not the issue here.
From my perspective the more important question is:
What can you expect from a 3D to 2D projection.

This concerns especially the animal legs and I’ve tried to coarsely estimate the maximum area deviation as ±10%. Feel free to tell me your estimated range.

For the sample image, both results deviate for different reasons but the deviations are much smaller than ±10%. My conclusion is that both methods are reasonable because they produce results that are within a range of uncertainty that is independent of the applied method and more or less given by the animal position.

My estimation of the projected animal area of 7.3±0.4cm^2 is from an analysis of the deviations produced by both methods.
Grid-removal: wrongly missing area
Grid-erosion: wrongly included area (left front-leg and shadows)



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  • Copy and paste the block of code I wrote above.
  • Choose File > New > Script… from the Fiji menu.
  • Choose Languages > ImageJ1 Macro from the Script Editor menu.
  • Paste the copied text into the Script Editor window.
  • Click the Run button to run it.
  • You can also File > Save as… and name it whatever you want ending in .ijm (e.g. Segment_Excluding_Grid.ijm).
  • To make it available in the menus all the time, create a folder and place the macro file there, then restart Fiji. The command will then appear at Process > Segment Excluding Grid.

See this documentation for further details.

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