Posted by
Michael Miller on
URL: http://imagej.273.s1.nabble.com/Plugin-threshold-ROI-tp3701007p3701008.html
Hello everyone,
I've been working with Liisa quite a bit. I think I can clear a few things
up.
For some samples of her images see:
http://img132.imageshack.us/img132/6105/t2img100jl2.pnghttp://img132.imageshack.us/img132/4930/t2img1cb9.pngWhat she needs is the exact origin/center of the dark circles. Her images
are all square width/height but the dark circles are not all exactly
centered relative to her images. We've gotten a basic diffuse subtraction
working in a custom plugin but it would work a lot better if we could start
it from the origin of the dark circle. What we need is some procedure or
Java method that we could run to get the approx origin.
The dark circles "darkness" changes typically within 18 +/- 4 but that may
change per image, they can be offset both in x and y but should be
approximately centered, and I'm fairly certain they stay around radius 50.
One idea I had was to use the analyze particles "center of mass" measurement
would be perfect for extracting this info. We can set threshold to 5 - 25 or
so, and analyze particles to 2500 - 10000 or something and grab the center
circle.
Another was to draw two ROI lines, plus shaped, through the middle of the
picture. A PlotProfile would reveal the approximate center of the circle.
This method is axis/directional dependent however :-(
-Mike
----- Original Message -----
From: "Liisa Palomaa" <
[hidden email]>
To: <
[hidden email]>
Sent: Sunday, November 12, 2006 1:54 PM
Subject: Plugin- threshold, ROI
> Hi everyone!
>
> I need help to modify a plugin so I can adjust the threshold- ( I
> can't get the plugin thresholdadjuster to work!) - Then I want the
> threshold to be a ROI- so I can find the center of the thresholded
> area. Is that possible in a plugin?
>
> It would be good if the plugin works for stacks.
>
> Best regards
> //Liisa