How to calculate area of a particle that contains abundant irregular inclusions

[crystal_analysis]

Hello,
          I have a series of images from mineral crystals. The images show the element content of the various mineral phases. I want to calculate the proportion of area covered by a certain intensity. For instance, in the example below I want to calculated the area covered by the mineral with the orange level of intensity.

So, I transformed the image in an 8-bit format.



Then, using the threshold function I merged the blue intensity with the background. Finally I turned the image into a binary image. But, from there I have not been able to calculate the area of only the white intensity pixels. I want to exclude the area of inclusion within the large crystals. I think that the fact there are many small irregular inclusions prevents Image J from doing a proper calculation. When I try the analyze particles function and check the outlines box, Image J calculate an area from a bunch of the small inclusions, but does not calculate the large crystals.... If you have any suggestion for a proper procedure please let me know. Thanks a lot

Cheers

[Krs5]

Dear ??

Looks like you are almost there. If you analyse the particles and you don't select 'include holes', it should give you the results without the holes. If you select 'include holes' you will find a larger area, as now the holes are included as part of your selected areas. In the example it should read 43.8% as fraction.


Hope this answers your question

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of crystal_analysis
Sent: 08 April 2011 15:57
To: [hidden email]
Subject: How to calculate area of a particle that contains abundan irregular inclusions

Hello,

          I have a series of image from mineral crystals. The images show
the element content of the various minerals phases. I want to calculate the
proportion of area covered by a certain intensity. For instance, in this
example I want to calculated the area covered by the mineral with the orange
level of intensity
http://imagej.588099.n2.nabble.com/file/n6254050/Crystals_Original.jpg 




http://imagej.588099.n2.nabble.com/file/n6254050/Crystal_Binary.jpg 

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[crystal_analysis]

Hello Dr. Straatman,
                             Thank You Very Much for answering my question. I followed your instructions and I can now routinely carry out the area calculations that I need.
Sincerely,
Simon.

[Krs5]

Dear list members,

I will organize two one day ImageJ workshops 'Introduction to ImageJ' on 21 July and 'Writing macros in ImageJ' on 22 July 2011 at the University in Leicester, UK.

The workshops are focussed on scientists who want to use or have started to use ImageJ but are not sure how to make best use of it.

Please visit http://www.le.ac.uk/biochem/microscopy/ImageJ2011.html for further information.

Best wishes

Kees

Dr Ir K.R. Straatman
Senior Experimental Officer
Centre for Core Biotechnology Services
College of Medicine, Biological Sciences and Psychology
http://www.le.ac.uk/biochem/microscopy/home.html

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of crystal_analysis
Sent: 15 April 2011 19:43
To: [hidden email]
Subject: Re: How to calculate area of a particle that contains abundan irregular inclusions

Hello Dr. Straatman,
                             Thank You Very Much for answering my question.
I followed your instructions and I can now routinely carry out the area
calculations that I need.
Sincerely,
Simon.

--
View this message in context: http://imagej.588099.n2.nabble.com/How-to-calculate-area-of-a-particle-that-contains-abundant-irregular-inclusions-tp6254050p6277296.html
Sent from the ImageJ mailing list archive at Nabble.com.

[Dr Sabrina Lo Brutto]

Dear Colleagues and Friends

we are pleased to announce the forthcoming MEB Conference "NEW FRONTIERS FOR
MONITORING EUROPEAN BIODIVERSITY: THE ROLE AND IMPORTANCE OF AMPHIPOD
CRUSTACEANS", which will be held in September 27th-29th, 2011 in Palermo,
Italy.

The themes of the meeting range from pure to applied topics, six main
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Session 1 New needs, Old tools: how taxonomy can help in monitoring the
present-day biodiversity changes.

Session 2   How much diversity in Amphipoda (morphotypes, ecotypes, trophic
categories).

Session 3   Novel interactive tools recently developed and based on
morphological characters.

Session 4   Novel interactive tools recently developed and based on
molecular characters.

Session 5   Examples of the use of the taxon Amphipoda in environmental
monitoring.

Session 6 How decline in popularity of traditional taxonomy could impact on
biology and society and which agencies support taxonomic research.


Online Registration is Now Open!

Visit http://www.meb-conference.com/

On behalf of the conference organisers, we hope to see you there!

Kindest regards

Sabrina Lo Brutto


Please, feel free to forward this first announcement to all those who could  
be interested in the topic.


--
Dr Sabrina Lo Brutto
Dipartimento di Biologia Ambientale e Biodiversità
University of Palermo
via Archirafi 18
90123
Palermo
Italy
tel [phone]
fax [phone]