How to perform watershed on this image

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How to perform watershed on this image

Rohitesh Gupta
Hi All,

I want to show distinction between cellular layer and non-cellular space on this image. Probably create a contrast and then apply watershed. Could anyone help on this.

Thanks,
Rohitesh

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Colony_B3GNT3_Clone1_1.jpg (20K) Download Attachment
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Re: How to perform watershed on this image

Rohitesh Gupta
Hi All,

This is the corrected image.

Thanks,
Rohitesh

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B3GNT3 C1 S1-1 24H.jpg (556K) Download Attachment
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Re: How to perform watershed on this image

Krs5
Dear Rohitesh,

The below macro code is doing more or less what you want on the image you submitted. No idea if it will work on other images you have but give it a go

title = getTitle();
run("Duplicate...", " ");
run("8-bit");
run("Bandpass Filter...", "filter_large=40 filter_small=3 suppress=None tolerance=5 autoscale saturate");
run("Find Edges");
run("Find Edges");
run("Find Edges");
run("Auto Local Threshold", "method=Contrast radius=15 parameter_1=0 parameter_2=0 white");
run("Select All");
run("Enlarge...", "enlarge=-1");
run("Crop");
run("Analyze Particles...", "size=25000-Infinity add");
selectWindow(title);
roiManager("Show All without labels");

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility

ImageJ workshops 15 and 16 July, Leicester, UK. For registration visit https://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/AIF/workshops/imagej-workshops-July-2019


-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Rohitesh Gupta
Sent: 09 April 2019 01:02
To: [hidden email]
Subject: Re: How to perform watershed on this image

Hi All,

This is the corrected image.

Thanks,
Rohitesh

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ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&amp;data=02%7C01%7Ckrs5%40leicester.ac.uk%7C35f0bbd965d044c506ce08d6bc7ed566%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636903650269547352&amp;sdata=%2FpB3PijyzKOR1rdpAXgZC68LavHifZbyPHNoeBVeu0c%3D&amp;reserved=0

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Re: How to perform watershed on this image

Rohitesh Gupta
Hi Kees,

The code works just fine. I will work on it further.

Thanks for all the help.
Rohitesh

-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Straatman, Kees (Dr.)
Sent: Tuesday, April 9, 2019 3:10 AM
To: [hidden email]
Subject: Re: How to perform watershed on this image

Dear Rohitesh,

The below macro code is doing more or less what you want on the image you submitted. No idea if it will work on other images you have but give it a go

title = getTitle();
run("Duplicate...", " ");
run("8-bit");
run("Bandpass Filter...", "filter_large=40 filter_small=3 suppress=None tolerance=5 autoscale saturate"); run("Find Edges"); run("Find Edges"); run("Find Edges"); run("Auto Local Threshold", "method=Contrast radius=15 parameter_1=0 parameter_2=0 white"); run("Select All"); run("Enlarge...", "enlarge=-1"); run("Crop"); run("Analyze Particles...", "size=25000-Infinity add"); selectWindow(title); roiManager("Show All without labels");

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility

ImageJ workshops 15 and 16 July, Leicester, UK. For registration visit https://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/AIF/workshops/imagej-workshops-July-2019


-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Rohitesh Gupta
Sent: 09 April 2019 01:02
To: [hidden email]
Subject: Re: How to perform watershed on this image

Hi All,

This is the corrected image.

Thanks,
Rohitesh

--
ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&amp;data=02%7C01%7Ckrs5%40leicester.ac.uk%7C35f0bbd965d044c506ce08d6bc7ed566%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C636903650269547352&amp;sdata=%2FpB3PijyzKOR1rdpAXgZC68LavHifZbyPHNoeBVeu0c%3D&amp;reserved=0

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