Questions about analyze particles

Posted by Ruszkai Ákos on Nov 29, 2009; 3:33pm
URL: http://imagej.273.s1.nabble.com/Questions-about-analyze-particles-tp3690273.html

Hello,

First of all, let me introduce myself: I'm Ruszkai Ákos, a Hungarian
graduate pharmacist student. I'm writing my thesis about "Image analysis in
medicine technology".
I'll compare two different softwares (ImagePro + and ImageJ), in their
features and the results they return. In the laboratory, we mainly use
ImagePro+,so I'd like to focus more on ImageJ.Though I've read the online
manual, I still have some questions about the process and the results that
ImageJ returns. This'll be a long post to read, so sorry about that.
First, I'd like to ask what's the best pick to install: daily builds, or
stable versions? I'm using ImageJ on Debian testing, so I'm not unfamiliar
with handling with bugs and problem solving, in case things go wrong. Until
today, I've used 1.43g (that was installed from debian repository), but I
could upgrade to 1.43l via the built-in upgrader.
My following questions are about the analysis, and the results it returns,
because some things are quite confusing.
To describe in short, I need to analyse medicine pellets from digital photos
my consultant has provided me from the lab. I need to measure their "shape
descriptors", and the basic parameters (area, centroid, Feret etc.) I'm not
sure whether is this a bug or a feature, but I've noticed that the results
do not follow each other exactly as they were selected in the Set
Measurements dialogue. For example, Feret has 5 columns to display the
results: Feret, FeretX, FeretY, FeretAngle, MinFeret. The problem is, that
the Slice results column comes in between Feret and FeretX. This is not a
real problem, but I think it would be easier to look at the results if they
were sorted. Is this a bug, or am I missing an option checked in?
To get the proper statistical results, I need to measure circa 250 pellets
for each test. I've found, that this task is very easily done with the
stacks feature. The ROIs are easy to edit too, in case there's a dirt in the
image, that the auto threshold can't detect. So in the end, I get a stack
with 10 images, and approx. 250 ROIs. While it's not necessary, but it would
be nice to look at and draw only the ROIs on each slice - I can't do this
with the "show all" function, because that'll draw all ROIs on the same
slice, and that provides a complete mess. Is it possible to draw  ROIs that
belong to a particular slice only?
My third question is the most serious one, as I just can't figure out how
the "Summarise" works in the Results table.
In the attached image, my problem is clear: it seems, that the results are
shifted after "Feret". There are two columns with "-" that creates this
problem. Ok, I can clear those and move the columns back to ther places in
OpenOffice Calc, you can see that in xls I've uploaded to:

http://akion.planetnexuiz.de/sote/thesis/full_results.xls

Look at the end of the results: where does that very last column come from
(in coumn X) ? I can't even see that in the Results table in ImageJ.
I hope my letter isn't that long, and I'm not asking too basic things.
Thank you for your support.

Best regards,

Ákos