I have images where i want to create a macro, and part of this would include having fiji select all pixels of a certain value (8bit color, for example select all pixels of unit 170). Any ideas?
If it is already grey scale, you should be able to threshold that and then analyze particles to make a mask, or ROIs, or whatever you want. Your threshold would be 170-170.
Thank you so much for the reply! This worked wonders in selecting the area with those pixels! The only problemim having is I can not find a way to select the area inside the selection. For example, when i set the threshold with the color values, it selects a 1x1 pixel of the colored circle. And when i go to measure the area it is measuring the circle (the 1x1 pixel circle) itself and not the area enclosed by the circle. any ideas how to have imagej select the inside/enclosed area?
Depending on how accurate you need to be, you could just fill holes, assuming the circles are distinct. your area would include the 1 pixel ring.
Otherwise you could threshold, create a mask, and invert, and then analyze particles on the remaining objects. That would include both inside and outside of the circle, so you would probably need to also threshold on circularity or area.
Not really that great with FIJI though, so maybe someone else will come along with a better suggestion.
Can you post an example. What do you mean a 1x1 pixel circle?
I meant a 1 pixel ring.Picture attached. I want the area that is enclosed within this ring, but it seems harder than i assumed.
This is what the whole thing looks like that ring surronds the area of interest.
Sorry, I do not understand what you mean by “rings” I see two convoluted curves.
By a “ring” I would expect a closed contour…
Once you obtained the thresholded pixels=170. what is the next step you are after?
Note that a thresholded set of pixels does not iimply that they enclose a region (imagine a set of lines or a skeleton without any loops).
Im sorry i reposted the picture. The selection using thresholds works but i need to have it select the area inside the line/circle The results i get are for the circle outline (not sure what to call this). For example the area of the inner circle enclosed by the lines should be 0.10 mm^2 but i get 0.001mm^2 for example, and if i maually select the area inside the circle i get the expected 0.10mm2.
Also the ruler measurments were put in manually, any ideas how to find the max vertical/horiztonal diameter of the shape itself, i dont need a rectangular bound size because i only want to measure straight line inside the shape. And Ferets measurments are maximum but i need max vertical/horiztonal.
Thank you so much for your help!
aa1.tif (609.0 KB)
If you are using the particle analyzer to get the area, then there is a setting to include the holes or not, maybe that is one source of the problem.
Also you need to create a selection from the thresholded setting (region of interest) before computing its area. For that you use: