Using ImageJ for bacteriophage plaques

[Tamara James]

I have a question regarding an auto detection or manual selection of
detected circles (bacteriophage Plaques)- I have attached the images here
and any help would be terrific.

http://forum.imagej.net/t/image-analysis-for-bacteriophage-plaques/2549?u=tamarajame

Thank you
Tamara

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[Aryeh Weiss]

On 22/08/2016 10:55 PM, Tamara James wrote:
> I have a question regarding an auto detection or manual selection of
> detected circles (bacteriophage Plaques)- I have attached the images here
> and any help would be terrific.
>
> http://forum.imagej.net/t/image-analysis-for-bacteriophage-plaques/2549?u=tamarajame
>
>

Try the following macro with your image open:

inputTitle = getTitle();
run("8-bit");
run("Duplicate...", " ");
rename("bg");
bgTitle = getTitle();
run("Gaussian Blur...", "sigma=50");

imageCalculator("Subtract create", bgTitle, inputTitle);
resultTitle = getTitle();

run("Enhance Contrast", "saturated=0.35");
setAutoThreshold("Default dark");
run("Analyze Particles...", "size=100-Infinity  show=Masks display
exclude clear summarize add");
maskTitle = getTitle();
run("Grays");
selectWindow(inputTitle);
roiManager("Show All without labels");

You may need to do some tweaking, but this should get you started.
Let me know if you have trouble running this.

--aryeh

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Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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[Krs5]

Dear Tamara,

You could try

selectWindow("LargePlaqueExample(July30th).png");
run("Median...", "radius=4");
run("Find Maxima...", "noise=8 output=[Maxima Within Tolerance] exclude light");
run("Analyze Particles...", "size=5-Infinity show=Nothing display summarize add");
selectWindow("LargePlaqueExample(July30th).png");
roiManager("Show All without labels");

You can change the radius of the Median filter (or use a different filter) and/or the noise setting in Find Maxima to optimize the results.

Good luck

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Tamara James
Sent: 22 August 2016 20:55
To: [hidden email]
Subject: Using ImageJ for bacteriophage plaques

I have a question regarding an auto detection or manual selection of detected circles (bacteriophage Plaques)- I have attached the images here and any help would be terrific.

http://forum.imagej.net/t/image-analysis-for-bacteriophage-plaques/2549?u=tamarajame

Thank you
Tamara

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Jan Eglinger]

Dear all,

please note that there also were several answers to the post on the
ImageJ forum. To allow others to follow, I'm posting the link again:

http://forum.imagej.net/t/image-analysis-for-bacteriophage-plaques/2549

Jan


On 23.08.2016 09:46, Straatman, Kees (Dr.) wrote:

> Dear Tamara,
>
> You could try
>
> selectWindow("LargePlaqueExample(July30th).png");
> run("Median...", "radius=4");
> run("Find Maxima...", "noise=8 output=[Maxima Within Tolerance] exclude light");
> run("Analyze Particles...", "size=5-Infinity show=Nothing display summarize add");
> selectWindow("LargePlaqueExample(July30th).png");
> roiManager("Show All without labels");
>
> You can change the radius of the Median filter (or use a different filter) and/or the noise setting in Find Maxima to optimize the results.
>
> Good luck
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Advanced Imaging Facility
> Centre for Core Biotechnology Services
> University of Leicester
> http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Tamara James
> Sent: 22 August 2016 20:55
> To: [hidden email]
> Subject: Using ImageJ for bacteriophage plaques
>
> I have a question regarding an auto detection or manual selection of detected circles (bacteriophage Plaques)- I have attached the images here and any help would be terrific.
>
> http://forum.imagej.net/t/image-analysis-for-bacteriophage-plaques/2549?u=tamarajame
>
> Thank you
> Tamara
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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