Posted by
Kenneth Sloan-2 on
Sep 01, 2010; 3:27am
URL: http://imagej.273.s1.nabble.com/hacking-help-please-tp3687063.html
I would appreciate pointers, clues, and hints on how to do the following:
a) outline a large, blob-like region in an image
b) within that region, outline MANY small included regions
c) report:
for the large blob: area
for EACH small included blob:
centroid
area
integrated intensity
d) subtract all of the included blobs from the large blob, and then report:
remaining area
integrated intensity over that area
I can see most of the pieces by pointing and clicking and reading the manual - but it would really help
to see something close to an actual implementation.
My immediate stumbling blocks are:
* displaying the enclosing blob boundary AND the boundaries of all the smaller blobs
(my problem is that I can only see the current blob - which then disappears when I start on the next one)
* details on managing the results
I'm probably more comfortable writing Java code - but I'd be happy to try to do this as a macro.
I'll probably want to use a polygon for the large blob boundary - and fit ellipses to the smaller blobs.
If you care - what I'm measuring are cone inner segments in human retina and mitochondria. (actually, someone else will sit
at the image and count them - I'm the GUI guy).
To calibrate - I've been creating systems to help people make these sorts of measurements for some 30+ years, and am comfortable writing fairly complicated pieces of Java code - what I need help on are the nitty gritty details.
(perhaps all I need are pointers of the form: "check out tutorial #'s 3, 5, 11, and 43")
Thanks very much - all clues gratefully accepted.
With luck, I can demo the resulting system, and show off some results, in Luxembourg.
--
Kenneth Sloan
[hidden email]