Thresholding of PT Nanoparticles

[Thomas Sadowski]

Hello all,
 
I am currently involved in a research project that seeks to count a large number of platinum nanoparticles imaged via TEM in to obtain size distribution data. We are beginning by repeating the procedure illustrated in the paper "Computer-Based Analysis of Nanoparticle Transmission Electron Microscopy Data Using a Public Domain Image-Processing Program, Image" written by Woehrle, Hutchison, et al. submitted to the journal Material Characterization. Unfortunately the images with which we are working with have relatively few nanoparticles dispersed on a grid, as such problem arise when we threshold prior to particle analysis. My questions are:
 
1. Has anyone else had experience with using ImageJ to analyze any type of nanoparticle. If so I would be interested to hear any problems of comments you may have.
 
2. I believe that we need a local thresholding algorithm in order to adequately deal with these samples and avoid was out by the background deposition grid. Does anyone know of a good algorithm of is there one previously coded that I could use??
 
Thank you once again. Any comments, no matter how small would be very much appreciated.
 
Thomas Sadowski
Southern Connecticut State University

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[Albert Cardona]

Thomas,

You could write or record a very simple macro that:
- sets a rectangular ROI of a given width and height at 0,0
- applies threshold (so it is local)
- moves the ROI one width, or one height and to x=0 when going beyond the right
side of the image.

If you are into math, you could even overlap to whatever extent the ROI for
thresholding and store the result elsewhere (not on the image itself), and then
compute the best threshold from the ovelaps, according to the distribution
function of your choice.

Albert

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[Huw Blackwell]

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I use ImageJ to measure particles down to the order of hundreds of
nanometers on silicon using an SEM. These can go down to 10s of
nanometer, but I don't work that small. As I understand it, as long as
your equipment can produce a relatively decent image, then imageJ ought
to be able to handle it. I occasionally have problems whereby the
threshold algorithm highlights the background, rather than the
particles, but this can be resolved or either by setting the threshold
manually, or better I found by actually setting the contrast higher on
the SEM. I actually have a simple Macro which now does the thresholding,
particle count and distribution in one click just to avoid tiresome
repeats. What specific problems are you having with your thresholding?

Huw

Thomas Sadowski wrote:

> Hello all,
>  
> I am currently involved in a research project that seeks to count a large number of platinum nanoparticles imaged via TEM in to obtain size distribution data. We are beginning by repeating the procedure illustrated in the paper "Computer-Based Analysis of Nanoparticle Transmission Electron Microscopy Data Using a Public Domain Image-Processing Program, Image" written by Woehrle, Hutchison, et al. submitted to the journal Material Characterization. Unfortunately the images with which we are working with have relatively few nanoparticles dispersed on a grid, as such problem arise when we threshold prior to particle analysis. My questions are:
>  
> 1. Has anyone else had experience with using ImageJ to analyze any type of nanoparticle. If so I would be interested to hear any problems of comments you may have.
>  
> 2. I believe that we need a local thresholding algorithm in order to adequately deal with these samples and avoid was out by the background deposition grid. Does anyone know of a good algorithm of is there one previously coded that I could use??
>  
> Thank you once again. Any comments, no matter how small would be very much appreciated.
>  
> Thomas Sadowski
> Southern Connecticut State University
>
> _________________________________________________________________
> It’s the future of Hotmail: Try Windows Live Mail beta
> http://www2.imagine-msn.com/minisites/mail/Default.aspx?locale=en-us

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[Joachim Wesner]

Hi there,

only my 2 cents....

wouldn´t the "rolling ball" algorithm under "Process/Subtract
background..." already do most of the job?

JW



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Thomas,

You could write or record a very simple macro that:
- sets a rectangular ROI of a given width and height at 0,0
- applies threshold (so it is local)
- moves the ROI one width, or one height and to x=0 when going beyond the
right
side of the image.

If you are into math, you could even overlap to whatever extent the ROI for
thresholding and store the result elsewhere (not on the image itself), and
then
compute the best threshold from the ovelaps, according to the distribution
function of your choice.

Albert

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[Gary Chinga]

Difficult to segment the particles from the noisy background, but try  
the following, seems to work:

1.- Crop the image to comprise only the area for analysis.
2.- Process/Subtract background... r=5 pixels for the first image and  
r= 10 pixels for the second image.
3.- Process/Filters/Median, r=1 pixel.
4.- Threshold. The thresholding algorithm in the IJ program doesnt  
work with this type of images. Try the Entropy thresholding plugin by  
jarek Sasha (http://rsb.info.nih.gov/ij/plugins/entropy.html) seems  
to work well. There is also another thresholding procedure that may  
work if necessary.
5.- Run the Shape descriptor plugin (www.gcsca.net). You may want to  
filter out small particles and large agglomerates by varying the size  
and form factor of the particles, i.e. size: 4-infinity and form  
factor: 0.8-1.0. Check the "Clear particles" option.

This is a start and may need some tuning for best results. I hope  
this helps.

Gary.




On Jun 7, 2006, at 1:38 AM, Thomas Sadowski wrote:

> Hello all,
>
> I am currently involved in a research project that seeks to count a  
> large number of platinum nanoparticles imaged via TEM in to obtain  
> size distribution data. We are beginning by repeating the procedure  
> illustrated in the paper "Computer-Based Analysis of Nanoparticle  
> Transmission Electron Microscopy Data Using a Public Domain Image-
> Processing Program, Image" written by Woehrle, Hutchison, et al.  
> submitted to the journal Material Characterization. Unfortunately  
> the images with which we are working with have relatively few  
> nanoparticles dispersed on a grid, as such problem arise when we  
> threshold prior to particle analysis. My questions are:
>
> 1. Has anyone else had experience with using ImageJ to analyze any  
> type of nanoparticle. If so I would be interested to hear any  
> problems of comments you may have.
>
> 2. I believe that we need a local thresholding algorithm in order  
> to adequately deal with these samples and avoid was out by the  
> background deposition grid. Does anyone know of a good algorithm of  
> is there one previously coded that I could use??
>
> Thank you once again. Any comments, no matter how small would be  
> very much appreciated.
>
> Thomas Sadowski
> Southern Connecticut State University
>
> _________________________________________________________________
> It’s the future of Hotmail: Try Windows Live Mail beta
> http://www2.imagine-msn.com/minisites/mail/Default.aspx?locale=en-us
>