Re: processing of noisy images with particles in bad contrast

Posted by Jean-Philippe Grossier on
URL: http://imagej.273.s1.nabble.com/processing-of-noisy-images-with-particles-in-bad-contrast-tp5013824p5013836.html

Hi,

I tried to subtract two gaussian with a small and a big radius and it gives
decent results:

makeRectangle(13, 41, 470, 445);
run("Crop");

run("Duplicate...", "title=bigGauss duplicate");
run("Invert", "stack");
run("Gaussian Blur...", "sigma=15 stack");


selectWindow("particles_anim.tif");
run("Duplicate...", "title=smallGauss duplicate");
run("Invert", "stack");
run("Gaussian Blur...", "sigma=5 stack");

imageCalculator("Subtract create stack", "smallGauss","bigGauss");
selectWindow("Result of smallGauss");
setMinAndMax(9, 11);



you can play with the radius to get better result I guess.

Jean-Philippe

2015-07-31 9:10 GMT-04:00 J. Sedgewick <[hidden email]>:

> A deceptively easy way to improve contrast and remove noise can be done
> through resampling. If you scale (resample) your image to a less pixels
> across and down (say 25% of its original pixel resolution) then resample
> again to enlarge it back to its original size, you'll see the black spots
> sans noise (if these are the ones that are larger in your image).
> Experiment with different resampling percentages to get the desired result.
>
> Jerry
>
> -----Original Message----- From: M S
> Sent: Friday, July 31, 2015 7:30 AM
> To: [hidden email]
> Subject: processing of noisy images with particles in bad contrast
>
>
> Good day, dear ImageJ users!
> My field of work is totally not related to image processing, but
> therealways is a first time when you need to do something new. Having no
> idea how toproceed makes it difficult though.
> I have acquired many images similar to what can be seen in particles.tif.
> Ifyou use your imagination then you can see approximately 58 black blobs
> which Ihave marked in markers_particles.tif. The problem is that very low
> exposition wasused (since the particles move really fast) and that creates
> all the noisewhere actual particles are drowning.
> I have played with ImageJ/Fiji settings – Image arithmetics,
> Threshold,Enhance Contrast, Noise removal etc. in different combinations,
> but nothingbrings any satisfactory results. By satisfactory I mean more or
> less clearly visibleparticles that could be traced. If from these
> 50-something particles that canbe seen even half could be traced, that
> would be a great achievement. I haveattached a short preview of image
> sequence as well.
> So the question – is it possible to automatically process these
> imagesequences in not time consuming way (manual processing of single image
> is notwhere I would like to spend my time) so final result would be a clear
> view ofat least some particles which could be traced using for example
> Mosaic’sParticle Tracker?
> Sincerely,John
>
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