point selection and counting procedure

Posted by Thorsen, Anders on Oct 16, 2006; 11:53am
URL: http://imagej.273.s1.nabble.com/point-selection-and-counting-procedure-tp3701294.html

Hi,

We are counting oocytes from whole mount pictures of fish ovaries. We are
counting a lot of samples so our counting procedure should be as efficient
as possible. The majority of the oocytes (the dark vitellogenic ones) are
counted easily using the analyze particle function. However, after the
particle analysis has been run there is still some oocytes that have not
been counted. Mainly this is the previtellogenic oocytes that are
transparent and difficult to threshold on. These oocytes have to be counted
manually on the picture. I find using the point selection tool is in many
cases efficient, however we should only count oocytes that are larger than
150 µm. That means that oocytes around this threshold value has to be
measured using the line tool to decide wether it should be counted or not.
Since this is a new type of measurement ImageJ then want to empty the
results window to make room for the new type of data, and this makes it very
cumbersome. We could of course do all the manual counting using the line
tool, but that would take much more time and we have a lot of samples.

I can think of two solutions to this: 1. Make ImageJ accept several types of
measurements in the Results window at the same time. 2. Let the point
selection tool (the cross) have a selectable size so that it can function as
a size reference when doing the point selection. I have looked for plugins
or macros that could help us with this but haven't found any. Is anybody
aware of something that could solve this problem? Is there somthing I am
doing wrong? Could a plugin be made to solve this?

Background:
We are an ICES working group that is responsible for making egg-production
estimates for mackerel and horse-mackerel in the North Sea and Norwegian Sea
from mature pre-spawning ovaries. The egg-production estimates are then
compared to the amount of pelagic eggs of these species that is actually
found (using plankton net) during the spawning season. From this the total
spawner biomass is calculated, and this again makes an important basis for
deciding the fishing quotas for these species.

thank you

anders

..................................
Anders Thorsen
Dr. Scient.
Senior Scientist
Recruitment Biology and Behaviour
Institute of Marine Research
Nordnesgaten 50
P. O. Box 1870 Nordnes
N-5817 Bergen, Norway
Phone: [phone]
Fax: [phone]
E-mail: [hidden email]