Posted by
Michael Schmid on
Jul 31, 2015; 2:48pm
URL: http://imagej.273.s1.nabble.com/processing-of-noisy-images-with-particles-in-bad-contrast-tp5013824p5013831.html
Hi John,
it's so noisy that it is difficult to decide what is a blob and what isn't.
For processing, first you have to get rid of the margins with their different contrast. Then some combinations of filtering and smoothing will give at least some reasonable result. This is what I tried:
makeRectangle(6, 22, 487, 470);
run("Crop");
setThreshold(254, 255);
run("Create Selection");
run("Smooth");
run("Select None");
run("Smooth");
run("Remove Outliers...", "radius=3 threshold=20 which=Bright");
run("Gaussian Blur...", "sigma=2");
run("Maximum...", "radius=1");
run("Subtract Background...", "rolling=10 light");
setAutoThreshold("MaxEntropy");
Then run 'Analyze Particles' with a minimum size of your choice, depending on what minimum size you consider a true blob, not just noise.
Michael
________________________________________________________________
On Jul 31, 2015, at 14:30, M S wrote:
> 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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http://imagej.nih.gov/ij/list.html<particles_anim.tif><markers_particles.tif><particles.tif>
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