Help in measuring area with the 'wand'

measure
imagej
segmentation
#21

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

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#22

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)

HTH

Herbie

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#23
  • 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 Fiji.app/scripts/Process 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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