Newbie - Red Blue Black Image Easy Segmentation

Image Analysis
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#1

Background

Two fluids, one in red, the other in blue, and rocks in black.

Analysis goals

Get small blue segments extracted together with their area, number, as well as be able to fit an ellipse on each segment and get their corresponding small and large radii - Also get the total red, blue, and black area.

Challenges

  • What stops you from proceeding? I’m a newbie, haven’t been able to achieve my goal with the tutorials I see online
  • What have you tried already? thresholding, but cannot get the segments
  • What software packages and/or plugins have you tried? Fiji

Can someone please help me with how I can get small blue segments extracted together with their area, number, as well as be able to fit an ellipse on each segment and get their corresponding small and large radii - Also get the total red, blue, and black area.

circle_M1_Ca_Res_72_np24-201 2
circle_M1_Ca_Res_72_np24-201 21008×503 179 KB

#2

dear @soheilesm
You should be able to segment the red, blue and black segments separately with by using the Color Threshold plugin. Select the B&W overlay option. Then you can use the Analyze Particles plugin and select Summarize to get the overall area of the blue/red/black areas. Looking at the data, it appears their are black lines between the red and blue segments which will be counted in the final area total. I don’t know if that will be an issue.

If you manage to segment the blue channel, you can then use the Analyze Particles plugin to get the area/number of blue areas. Limit the size of the particles to exclude the larger blue segment.

To apply the ellipse to the blue segments, again use Analyze Particles and select Ellipse under Show. To get the major and minor radius of the ellipses, go to the Set Measurements plugin and select Fit ellipse and Shape Descriptor.

I hope this helps

#3

I doubt that the provided sample image is real-world data.
Please always post typical unprocessed images in the original uncompressed format.

Instead of using “Color Threshold” I recommend CMYK color space conversion. Then …

… the Cyan-channel gives the blue area,
… the Magenta-channel gives the black dots area, and
… the Yellow-channel gives the red area.

Fitting ellipses to the areas doesn’t conform with any reasonable null-hypothesis.