Basic Image J Help

[jkaufman]

Hi all,
I am a new user of Image J and a beginner programmer.  Eventually I want to create a plugin that can take a lapshear panel and spit out what percentage of the surface area is covered in adhesive and what percentage is just the aluminum panel. However for a beginner such as myself, I believe I should probably be starting smaller.  
Right now I am drawing a rectangle over the area, and using the free-hand tool to find the area of the adhesive and divide the two measurements to get a percentage.  My first question is does it make much of a difference if I use a plugin or a macro? Also, what tool or simple command can I write that will allow the plugin or macro to automatically find the area of an adhesive? Is there a way to find the edge between the aluminum and the adhesive?
I am currently trying to get a simpler problem to work smoothly. I am not 100% sure how to start though.
How would I find the area percentage of the cell colonies or of the blobs from the sample pictures from ImageJ?
Also if anyone has some good basic tutorials for the type of analysis (separation of distinct colors) that would be a great help.

Thank you for your time and help
Jonathan

[Nathaniel Ryckman]

The general process for detecting regions of interest (ROI's) is:
Threshold or Edge Detection -> Binarize -> Watershed/Fill/Etc -> Particle Analysis -> Measure

I personally think that this site has a good tutorial that gives you thorough examples without getting bogged down in detail:
http://www.macbiophotonics.ca/imagej/

Here's an e-mail that contains websites with more detailed documentation that I sent one of my co-workers who was interested in imageJ:

"Here is the official webpage for the original imageJ software documentation:
http://rsbweb.nih.gov/ij/docs/index.html

Here is a direct link to the important stuff. These are the "tools"
that I was talking about:
http://rsbweb.nih.gov/ij/docs/macro_reference_guide.pdf

Here is another direct link to more important stuff. This explains
functions, for loops, and other general programming concepts:
http://rsbweb.nih.gov/ij/developer/macro/macros.html

Here is another "flavor" of imageJ. There is additional documentation
that you can use from this site:
http://www.macbiophotonics.ca/imagej/

Here is another "flavor" of imageJ. There is also additional
documentation that you can use from this site:
http://pacific.mpi-cbg.de/wiki/index.php/Fiji"

[Nathaniel Ryckman]

jkaufman wrote

My first question is does it make much of a difference if I use a plugin or a macro?

Plugin allows you to have more control but macro is easier/quicker to create.

If you are creating a large or thorough program, you probably would be better off with the plugin. If you are doing something that you could do by using the menu commands in imageJ, then you probably can just write your program in a macro.

An analogy would be Visual Basic for Applications vs Visual Basic.

[Albert Cardona-2]

> My first question is does it make much of a difference if I
> use a plugin or a macro?

For simple repetitive tasks use a macro. To create your own GUIs and
use libraries use a plugin.

> Also, what tool or simple command can I write that
> will allow the plugin or macro to automatically find the area of an
> adhesive? Is there a way to find the edge between the aluminum and the
> adhesive?


Try this:

http://pacific.mpi-cbg.de/Trainable_Segmentation


Albert

--
http://albert.rierol.net

[jkaufman]

thank you for your help it is much appreciated.