calculating number of particles per cluster

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calculating number of particles per cluster

Hediyeh Malekzad Sani Nobar

Hello,
I need to analyse several SEM images and calculate number of particles per
each cluster.
I have activated Biovoxxel feature which is for studying clusters but,
still I can not define clusters.
Could you please help me with applying right parameters?
Sample image is attached
Thank you and regards
Hediyeh (See attached file: nanocluster-1h grd-p13+1mm_013.png)
Materials Research and Technology (MRT) Department,
Nano-Enabled Medicine and Cosmetics Group (NEMC)

Luxembourg Institute of Science and Technology, LIST
Office G1.31
41, rue du Brill
L-4422 Belvaux, Luxembourg

Tel: (+352) 671104321


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nanocluster-1h grd-p13+1mm_013.png (2M) Download Attachment
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Re: calculating number of particles per cluster

Herbie
Good day!

Your sample image is noisy and not very well resolved for this task.

Attached please find a first analysis of one of the clusters.
<http://imagej.1557.x6.nabble.com/file/t380516/nanocluster-1h_grd-p13%2B1mm_013-1.png>
The cluster was low-pass filtered and then "Find Maxima..." with tolerance
10 was applied.

You may also experiment with bandpass-filtering.

Clusters themselves can be found after massive low-pass filtering.

Good luck

Herbie



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Re: calculating number of particles per cluster

Hediyeh Malekzad Sani Nobar

Dear Herbie,
Thanks for your email.
I could find maxima after(See attached file: Capture1.PNG) applying
bandpass. You can see the attached image, however, my question is how can I
count number of particles for each cluster automatically.
Because I need to know average number of particles for all the clusters in
this image and another 30 more images that I have. So, as you can imagine I
cant count it manually.
For spread particles, we can do it by analyze>analyze particles, but here I
need to do it for clusters.
Thank you and regards
Hediyeh
Materials Research and Technology (MRT) Department,
Nano-Enabled Medicine and Cosmetics Group (NEMC)

Luxembourg Institute of Science and Technology, LIST
Office G1.31
41, rue du Brill
L-4422 Belvaux, Luxembourg

Tel: (+352) 671104321






From: Herbie <[hidden email]>
To: <[hidden email]>
Date: 11/02/2019 11:48
Subject: Re: calculating number of particles per cluster



Good day!

Your sample image is noisy and not very well resolved for this task.

Attached please find a first analysis of one of the clusters.
<
http://imagej.1557.x6.nabble.com/file/t380516/nanocluster-1h_grd-p13%2B1mm_013-1.png
>
The cluster was low-pass filtered and then "Find Maxima..." with tolerance
10 was applied.

You may also experiment with bandpass-filtering.

Clusters themselves can be found after massive low-pass filtering.

Good luck

Herbie



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Sent from: http://imagej.1557.x6.nabble.com/

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


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graycol.gif (146 bytes) Download Attachment
Capture1.PNG (713K) Download Attachment
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Re: calculating number of particles per cluster

Herbie
As I've tried to explain, it's a two step process:

First get the clusters, then analyze one after the other.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Am 11.02.19 um 15:27 schrieb Hediyeh Malekzad Sani Nobar:

>
> Dear Herbie,
> Thanks for your email.
> I could find maxima after(See attached file: Capture1.PNG) applying
> bandpass. You can see the attached image, however, my question is how can I
> count number of particles for each cluster automatically.
> Because I need to know average number of particles for all the clusters in
> this image and another 30 more images that I have. So, as you can imagine I
> cant count it manually.
> For spread particles, we can do it by analyze>analyze particles, but here I
> need to do it for clusters.
> Thank you and regards
> Hediyeh
> Materials Research and Technology (MRT) Department,
> Nano-Enabled Medicine and Cosmetics Group (NEMC)
>
> Luxembourg Institute of Science and Technology, LIST
> Office G1.31
> 41, rue du Brill
> L-4422 Belvaux, Luxembourg
>
> Tel: (+352) 671104321
>
>
>
>
>
>
> From: Herbie <[hidden email]>
> To: <[hidden email]>
> Date: 11/02/2019 11:48
> Subject: Re: calculating number of particles per cluster
>
>
>
> Good day!
>
> Your sample image is noisy and not very well resolved for this task.
>
> Attached please find a first analysis of one of the clusters.
> <
> http://imagej.1557.x6.nabble.com/file/t380516/nanocluster-1h_grd-p13%2B1mm_013-1.png
>>
> The cluster was low-pass filtered and then "Find Maxima..." with tolerance
> 10 was applied.
>
> You may also experiment with bandpass-filtering.
>
> Clusters themselves can be found after massive low-pass filtering.
>
> Good luck
>
> Herbie
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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Re: calculating number of particles per cluster

Herbie
In reply to this post by Hediyeh Malekzad Sani Nobar
Attaches please fins a segmentation of the clusters.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Am 11.02.19 um 15:27 schrieb Hediyeh Malekzad Sani Nobar:

>
> Dear Herbie,
> Thanks for your email.
> I could find maxima after(See attached file: Capture1.PNG) applying
> bandpass. You can see the attached image, however, my question is how can I
> count number of particles for each cluster automatically.
> Because I need to know average number of particles for all the clusters in
> this image and another 30 more images that I have. So, as you can imagine I
> cant count it manually.
> For spread particles, we can do it by analyze>analyze particles, but here I
> need to do it for clusters.
> Thank you and regards
> Hediyeh
> Materials Research and Technology (MRT) Department,
> Nano-Enabled Medicine and Cosmetics Group (NEMC)
>
> Luxembourg Institute of Science and Technology, LIST
> Office G1.31
> 41, rue du Brill
> L-4422 Belvaux, Luxembourg
>
> Tel: (+352) 671104321
>
>
>
>
>
>
> From: Herbie <[hidden email]>
> To: <[hidden email]>
> Date: 11/02/2019 11:48
> Subject: Re: calculating number of particles per cluster
>
>
>
> Good day!
>
> Your sample image is noisy and not very well resolved for this task.
>
> Attached please find a first analysis of one of the clusters.
> <
> http://imagej.1557.x6.nabble.com/file/t380516/nanocluster-1h_grd-p13%2B1mm_013-1.png
>>
> The cluster was low-pass filtered and then "Find Maxima..." with tolerance
> 10 was applied.
>
> You may also experiment with bandpass-filtering.
>
> Clusters themselves can be found after massive low-pass filtering.
>
> Good luck
>
> Herbie
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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

boundaries_nanocluster-1h grd-p13+1mm_013.tif Segmented.png (34K) Download Attachment
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Toolsets file sort order

Glen MacDonald-3
In reply to this post by Herbie
The macro filenames appear sorted randomly when opening the Toolsets folder from the ‘>>’ icon on the Fiji toolbar.  Opening the directory from the Plugins>Macro>Install displays the macros properly sorted by name.

2018 MacBookPro, OS10.14.3, IJ 1.52i, Java 1.8_162.  Its been happening for awhile and on other Macs.  
Is this a setting I’ve missed?

regards,
Glen MacDonald
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