Anyone here good with photoshop and scripting?

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Anyone here good with photoshop and scripting?

Post#1 » Mon Jun 15, 2009 2:28 pm

OK, right now I have a summer internship assisting with research on trees. Part of the job involves working in the field and taking measurements of the trees and counting strobili (the pollen producing part of the tree). Counting strobili is the most tedious part of the job (some trees have several thousand), I have been given the go ahead to look into automating this task. I'm not sure if what I want to do can be done with photoshop or other software. What I'm thinking of doing is this:

-Take pictures of the tree to be counted and stitch them together in photoshop.
-Select a range of colors for the strobili - they are usually a distinctly different color from the rest of the tree. I'm pretty sure photoshop can select all pixels of a particular color, but can it select a range of colors?
-Use photoshop to determine the number of pixels in the selection.
-Divide the selected number of pixels by size of one strobili to determine the number of strobili on the tree. I know this count won't be 100% accurate, but neither is counting them by hand, we are really only looking for a close estimate.

Can scripting/batch processing be used to mostly automate this process? Is there any other software out there that would be better suited for this? Pattern recognition software that could do this would be great, but I'm not sure that actually exists.

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Post#2 » Mon Jun 15, 2009 3:21 pm

Oh, believe me, it does. My company sells image capture and analysis packages that work on everything from individual molecules on a slide to transistors on a microchip to bacteria moving around in a live tissue sample.

The trouble is that these systems tend to run in the four to five figure range. Very basic analysis software might set you back a few grand. They also require some expertise to operate, although there are lots of built in macros and functions to make the job easier - the more expensive the package, the better your tools, naturally.

Obviously, because I work for Olympus, I'm biased in its favor, but one of the packages we sell for this purpose is MetaMorph - ... lysis.html . This runs from $7-10K for the baseline software but is really, really advanced. (Edit: the link is to the manufacturer's page; Olympus is a reseller and our page is here.)

The specific feature you're talking about is called "particle counting", so some searches on that might turn up more information.

Edit 2: try this Google search: ... g+software

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Post#3 » Mon Jun 15, 2009 4:12 pm

if you know someone who is skilled with labview, you can use a camera and code to find those things. i for one am not that skilled in labview. however, labview is one of the best Data aquisition/analysis software packages in an engineers arsenal. you do need to code it yourself. i bet if you googled for something like that you could get some help. there also may be modules you can purchase within labview. i'm sure you have labview at school somewhere, and if you don't.... well im sorry. its a lot of work, but if you have some other engineeringy type folks around, you could write something that works relativly quickly.

nifty google search

might help. its a book about image processing with labview. and yes, i am very sure you can do it easily. if you don't know labview, i recommend at least getting familiar with it.

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Post#4 » Mon Jun 15, 2009 7:35 pm

Thanks for the suggestions. I'm pretty sure they're not going to want to spend $10k+ on software though. I'll be out in the field again tomorrow to take some pictures, I'll see if my ghetto photoshop method works.

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