How to calculate the particle area during dissolution?

[dkaras]

Hello all,
I attached a couple of typical pictures of the dissolution of particles under the microscope.As you can see bubbles are around the particle so it make it very difficult to separate them.What i basically want to do it to isolate the information of bubbles and particle as a function of time.I tried to use some commands of ImageJ but its a way far more complicated.Could you please anyone help me with that.
Thanks in advance,
Dimitris    
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[Anderson, Charles (DNR)]

Dimitris

Have you tried working with greyscale morphology, thresholding, and subtracting?  See whether this helps you get started.

Charles

open("D:\\Documents\\Pictures\\PartBubbles.tif");  // change path and filename
//setTool("rectangle");
makeRectangle(389, 294, 233, 207);
run("Crop");
run("Duplicate...", "title=open5");
run("Gray Morphology", "radius=5 type=circle operator=open");
setAutoThreshold("Default dark");
//run("Threshold...");
//setThreshold(98, 255);
run("Convert to Mask");
run("Invert");

imageCalculator("Subtract create", "PartBubbles.tif","open5");
selectWindow("Result of PartBubbles.tif");
rename("particle.tif");
imageCalculator("Subtract create", "PartBubbles.tif","particle.tif");
selectWindow("Result of PartBubbles.tif");
rename("BubblesRemoved.tif");
 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of d karampalis
Sent: Thursday, May 28, 2015 8:23 AM
To: [hidden email]
Subject: How to calculate the particle area during dissolution?

Hello all,
I attached a couple of typical pictures of the dissolution of particles under the microscope.As you can see bubbles are around the particle so it make it very difficult to separate them.What i basically want to do it to isolate the information of bubbles and particle as a function of time.I tried to use some commands of ImageJ but its a way far more complicated.Could you please anyone help me with that.
Thanks in advance,
Dimitris    
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Krs5]

Dear Dimitris,

I have attached a macro that more or less does what you asked, at least on the images you supplied. The macro will analyse images in a directory (there should only be images in the directory) and saves the ROIs for each image and the final results table. See if it works on different data sets and if it is good enough for what you want to do.

Best wishes

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


________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of d karampalis [[hidden email]]
Sent: 28 May 2015 14:22
To: [hidden email]
Subject: How to calculate the particle area during dissolution?

Hello all,
I attached a couple of typical pictures of the dissolution of particles under the microscope.As you can see bubbles are around the particle so it make it very difficult to separate them.What i basically want to do it to isolate the information of bubbles and particle as a function of time.I tried to use some commands of ImageJ but its a way far more complicated.Could you please anyone help me with that.
Thanks in advance,
Dimitris
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dkaras]

Dear Kees,
Thank your for your kind reply and your help.I run the macro for an image sequence because the dissolution videos comes as images, but unfortunately the results fluctuating.I was wondering if it is possible to share with you a couple of videos to have a look? I think it might helpful in order to make the current macro more accurate.Can we also save the images after the process in a separate folder?Thank you very much once again.
Kind Regards,
Dimitris Karampalis

> Date: Thu, 28 May 2015 21:12:59 +0000
> From: [hidden email]
> Subject: Re: How to calculate the particle area during dissolution?
> To: [hidden email]
>
> Dear Dimitris,
>
> I have attached a macro that more or less does what you asked, at least on the images you supplied. The macro will analyse images in a directory (there should only be images in the directory) and saves the ROIs for each image and the final results table. See if it works on different data sets and if it is good enough for what you want to do.
>
> Best wishes
>
> 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
>
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] on behalf of d karampalis [[hidden email]]
> Sent: 28 May 2015 14:22
> To: [hidden email]
> Subject: How to calculate the particle area during dissolution?
>
> Hello all,
> I attached a couple of typical pictures of the dissolution of particles under the microscope.As you can see bubbles are around the particle so it make it very difficult to separate them.What i basically want to do it to isolate the information of bubbles and particle as a function of time.I tried to use some commands of ImageJ but its a way far more complicated.Could you please anyone help me with that.
> Thanks in advance,
> Dimitris
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[dkaras]

Dear Charles,
Thank you for your immediate reply.I run the macro in a couple of pictures and it looks promising. The only problem that i have is when the particle size is big the bubbles are also big and their reflection is high so when i do the analysis its count them a particle.I was wondering if we can convert it in a batch mode because I'm analysing image sequences and also how can extract the data from the particle area and the bubbles in an excel folder?Is it possible to share with you a couple videos to have a look?Thanks a lot for your help.
Kind Regards,
Dimitris

> Date: Thu, 28 May 2015 19:43:05 +0000
> From: [hidden email]
> Subject: Re: How to calculate the particle area during dissolution?
> To: [hidden email]
>
> Dimitris
>
> Have you tried working with greyscale morphology, thresholding, and subtracting?  See whether this helps you get started.
>
> Charles
>
> open("D:\\Documents\\Pictures\\PartBubbles.tif");  // change path and filename
> //setTool("rectangle");
> makeRectangle(389, 294, 233, 207);
> run("Crop");
> run("Duplicate...", "title=open5");
> run("Gray Morphology", "radius=5 type=circle operator=open");
> setAutoThreshold("Default dark");
> //run("Threshold...");
> //setThreshold(98, 255);
> run("Convert to Mask");
> run("Invert");
>
> imageCalculator("Subtract create", "PartBubbles.tif","open5");
> selectWindow("Result of PartBubbles.tif");
> rename("particle.tif");
> imageCalculator("Subtract create", "PartBubbles.tif","particle.tif");
> selectWindow("Result of PartBubbles.tif");
> rename("BubblesRemoved.tif");
>  
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of d karampalis
> Sent: Thursday, May 28, 2015 8:23 AM
> To: [hidden email]
> Subject: How to calculate the particle area during dissolution?
>
> Hello all,
> I attached a couple of typical pictures of the dissolution of particles under the microscope.As you can see bubbles are around the particle so it make it very difficult to separate them.What i basically want to do it to isolate the information of bubbles and particle as a function of time.I tried to use some commands of ImageJ but its a way far more complicated.Could you please anyone help me with that.
> Thanks in advance,
> Dimitris    
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

     
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