Thanks for the help but I have around 100 such rods per image. Do you know of any tool which could automatically do it without the need of manually drawing lines. I have around 200 such images, hence I ask.

Without seeing an example image it is not really possible to say how best to approach this. However if you find that a threshold is able to detect your structures reliably then it is relatively straightforward. The commands could be:

- Analyze -> Set Measurements... - make sure 'Fit ellipse' and / or 'Feret's diameter' are selected (or anything else you want)

- Image -> Adjust -> Threshold... - use the slider or an automated method from the drop-down list to detect your structures

- Analyze -> Analyze Particles... - this will measure all connected-regions above the threshold; you likely want to select 'Display results' and 'Clear results'; you may also set a minimum size threshold at the top to remove small erroneously-detected structures.

The documentation for 'Set Measurements...' can help you choose which measurement makes most sense for your 'rod length' (e.g. Feret diameter or major axis length of a fitted ellipse might be appropriate):

http://imagej.nih.gov/ij/docs/menus/analyze.html#set

Then Analyze -> Summarize of Analyze -> Distribution... would be used to get the average length.

Depending on the complexity or your image other steps might be needed, e.g. to correct for an uneven background, clean up mis-detections from the thresholding, or separate merged detections.

Thanks Peter 

Did I you still need help with this? We are about to release a very powerful and intuitive 2D/3D image analysis package at MIPAR.us and I'd be happy to try an image to see if we an help you. MIPAR has been to tack image segmentation and analysis tasks for us that few other software could.

Thanks for the reply John,

I calculated the lengths by drawing lines manually using ImageJ. I can still share one of the images with you and would like to see how your image analysis software works. It might help me in further analysis.

Absolutely! Feel free to share an image and I'll take a look!