Re: Removing Parts of the Image Below a Threshold Size

Posted by amoghj on Nov 10, 2015; 6:56pm
URL: http://imagej.273.s1.nabble.com/Removing-Parts-of-the-Image-Below-a-Threshold-Size-tp3689834p5014909.html

Hi!
I was wondering if your main problem is to only get rid of all the small
particles.
If so, then you can threshold your image, and use the Analyze Particles
function under Analyze. You can then set the size cut-off (to exclude
smaller sized particles), and the circularity(to remove particles than are
'round'); and finally set the Show: option to Masks in the drop down menu,
and hit ok.
Now use the Image Calculator function under Process, and carry out the
operation AND. This should leave you with just the particles of your
interest.
PFA the recorded actions, the thresholded image and the final image with
just the areas of interest.

setAutoThreshold("Default");

//run("Threshold...");

run("Analyze Particles...", "size=60-Infinity circularity=0.00-0.60
show=Masks display clear summarize");

selectWindow("P#233-S59-(20-30)-01-274_progress_cropped.jpg");

resetThreshold();

imageCalculator("AND create", "Mask of
P#233-S59-(20-30)-01-274_progress_cropped.jpg","P#233-S59-(20-30)-01-274_progress_cropped.jpg");


Hope this helps!

Best,

Amogh

On Tue, Nov 10, 2015 at 1:12 PM, valenzul <[hidden email]> wrote:

> Hello,
> I know this is an old post. I have 8-bit gray scale LUT root scanned images
> that I'm trying to clean out of small "dots" "unshaped particles" (sawdust
> and soil particles). I just installed the latest version of Image J and
> download the morphology plug-ins and macros and unzipped them inside the
> plug-in folder as instructed on your web page. However, I have not had any
> success getting the macro to work. After I upload the image I run the macro
> "KeppparticlesInRange" and is giving me a message "Unrecognized command:
> "Particles8".
> I think where I'm confused is on the following statement/procedure
> "Partilces8 and Particles4 can delete particles less and larger than
> certain
> size in pixels". Do I'm missing a a step or another macro before trying to
> run the macro?
> Will this procedure erase the "particles" from the image after? Would it be
> possible to save the image with the erased particles? I need to run the
> cleaned image on other software to measure root lengths.
> I included an example of one of my images, all those dots are the particles
> I want to delete. I've been doing this manually using gimp but is taking a
> long time. I hope Image J can do that for me.
> Thanks for your help,
> Luis Valenzuela
> <
> http://imagej.1557.x6.nabble.com/file/n5014907/P%23233-S59-%2820-30%29-01-274_progress_cropped.jpg
> >
>
>
>
>
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> Sent from the ImageJ mailing list archive at Nabble.com.
>
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