I am looking for an automated method of image analysis that would aid us in a morphological analysis of histological cross-sections of Beetle tissues. The most promising approach that I managed to find was an AdaBoost and GVF Snake algorithm, but I would need some help with getting through the mathematical formulas to a software. Any advice?
http://www.uky.edu/~lya227/muscle.html
This looks like something ImageJ might be able to handle. Here's a chapter on "Automated Segmentation and Morphometry of Cell and Tissue Structures. Selected Algorithms in ImageJ":
http://rsb.info.nih.gov/ij/docs/pdfs/automated_segmentation_and_morphometry.pdf
Their examples are not quite the segmentation that was done in the muscle article you linked, but it might give you some starting points about algorithms to search for.
A google search for "ImageJ tissue segmentation" pointed me to the following Balloon Plugin for identifying cellular boundaries (possibly included in FIJI):
http://www.archiroot.org.uk/doku.php/navigation/balloonplugin
There is also a "Trainable Weka Segmentation" plugin, which is included in FIJI:
http://fiji.sc/Trainable_Weka_Segmentation
Thank you for your answer. I am familiar with the linked publication. Unfortunately the plugins you mentioned are far from perfect and do not cope well with the non-circular cells that we are facing especially with triangular or simular shapes. Of course we will try to put some effort in the implementation of those plugins and we will try to modify them to our needs but still it may prove futile so the search is still on ;)
you can use the mambaImage which a free software you can load at mambaimage.com
Just looking at both of the software now, thank you very much for the input.
I would defintely recommend you visit www.MIPAR.us.
It is very powerful and intuitive 2D/3D image analysis software written by scientists/end-users and is about to be released as a free trial on December 14th. You can sign up on the site as well as submit images/datasets to test.
There are many image analysis options available, but I think you may just find MIPAR to be something special if you give it a try!
It's been almost 2 years since I faced the problem and to date I was able to solve some with ImageJ and Matlab but I will most definitely check it out. Thanks for the heads-up John. I highly appreciate it.
Our company offer histology image analysis. We could analyze many tissue types such as muscle, lung, bladder, pancreas, breast, and much more. The variety of services range from cell detection, cell segmentation, classification, image cleaning, feature extraction and so much more to best fit the focus of your research.
Contact me at [email protected] if you are interested.
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