i've used ImageJ (http://rsbweb.nih.gov/ij/), which is an open source java script based programme. it can be easily adapted to automate many steps, especially with that quantity of needles per image. i have also seen some attempts to integrate ImageJ with R, and it's a large time investment to get the same output with ImageJ alone.

alternatively, i just found this: http://goo.gl/CTvWO which discusses image classification in R using both programs but i think this might be more oriented towards GIS type applications. i think 'rimage' might be another option.

Thanks a lot Dylan, I appreciate your assistance. I'll look into your suggetsions.

I have a small macro for automating the image processing, should you want it. i just downloaded Bio7 (http://bio7.org), which is a stand-alone program that integrates imageJ with R, which looks promising.

If ever in the future you need to do this again, and you can get the program, WinSeedle is useful. Scans and measures all in one shot, and spits out LAI values based on scans. But may not be useful to you depending on your ability to get and learn the programs.

Hi, if you send me your direct email, I will post this query in our upcoming Forest Information Update. Cheers, Mike Smith. [email protected]

I use a free soft, UTHSCSA ImageTool (http://compdent.uthscsa.edu/dig/itdesc.html). The outputs are given in excel or txt format which can be easily exported to R or Matlab

Rebecca Bowler - I have looked into Winseedle already but it is a expensive option, I would like to use an open source program instead but thanks for your input.

Mike Smith - Email address sent, thanks.

Daniel Moya - I will also look into your suggestion, thanks.

For measurement of LAI, I suggest using the equipment SunScan, which allows higher data calibarción, directly determines LAI