Measuring of sponge spicule microscopy images

Posted by eburell on May 03, 2011; 11:31am
URL: http://imagej.273.s1.nabble.com/Measuring-of-sponge-spicule-microscopy-images-tp3684624.html

Dear members,

I am currently attempting to use ImageJ to measure the length and width of spicules found in sponges as a part of an assigned project. Unfortunately I am new to the usage of ImageJ and image analysis in general. I have two questions regarding ImageJ and image analysis.

The main problem I am facing right now is that I am unable to, more or less automatically, create a useful ROI from an microscopy image of a spicule sample (automation being part of the assignment). The ROI I'm trying to create is an an outline or a skeleton of the spicule for measurement. Attempts to skeletonize or otherwise create a binary image from the source image has been unsuccessful partly because of a poor source image and partly because of little to no knowledge regarding these operations (though I suspect the nature of the spicule images might also contribute). I have noticed that using a skeleton-based method makes the measurement of spicule thickness impossible and I am unsure of how I should counter this issue.

Am I approaching this measuring problem correctly?
Is there any recommended practice for this type of ROI-building and measuring?
Are there any tutorials or other documentation that detail a similar measuring processes for spike-shapes?

A sample microscopy image from the set i was given can be seen here: (https://skitch.com/aiden/r7j81/img-7369)
A rough sketch of the ROI I'm attempting to build can be seen here marked in red: (https://skitch.com/aiden/r7j86/img-7369-edited)

Regards,
Eli