help for an image j newbie please

[k k]

hello
i am a grad student and have recently discovered that i need to calculate
total surface area as well as the surface area of the right and left
ventricle from a cross-sectional picture of a pig heart.  I am hoping image
j can help me out but have never used the software before.  I would like
the program to outline the outer and inner edges of the heart walls
automatically and then calculate the surface area of what has been
outlined. In the cross section image the ventricle chambers are "holes"
which I do not want included in the area calculation.  I tried following
the sample method of using the variegated leaf found here (
http://rsb.info.nih.gov/ij/docs/pdfs/examples.pdf), but I am having a hard
time separating the heart from the background in the image.  I will
ultimately need to perform these calculations for 150 images, so I am
hoping to automate this process as much as possible.

thanks for any assistance.

kathy

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[Jacqueline Ross]

Hi Kathy,

If you want assistance with your enquiry, you really need to provide an image as it's hard for us to know what the issue with your segmentation is. If you can post one somewhere, I'm sure someone will be able to assist you.

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of k k
Sent: Wednesday, 5 March 2014 4:18 p.m.
To: [hidden email]
Subject: help for an image j newbie please

hello
i am a grad student and have recently discovered that i need to calculate total surface area as well as the surface area of the right and left ventricle from a cross-sectional picture of a pig heart.  I am hoping image j can help me out but have never used the software before.  I would like the program to outline the outer and inner edges of the heart walls automatically and then calculate the surface area of what has been outlined. In the cross section image the ventricle chambers are "holes"
which I do not want included in the area calculation.  I tried following the sample method of using the variegated leaf found here ( http://rsb.info.nih.gov/ij/docs/pdfs/examples.pdf), but I am having a hard time separating the heart from the background in the image.  I will ultimately need to perform these calculations for 150 images, so I am hoping to automate this process as much as possible.

thanks for any assistance.

kathy

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[kgeorge]

I am fairly new to Image J and found the eBook "Image Processing with ImageJ" by Mateos-Perez and Pascau very helpful. It's certainly a good primer on automation macros and includes numerous samples. As suggested, an example image would be helpful. Perhaps "Inlcude Holes under the Analyze Partilces is of interest.

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