Re: point selection and counting procedure

Posted by Thorsen, Anders on
URL: http://imagej.273.s1.nabble.com/point-selection-and-counting-procedure-tp3701294p3701296.html

Hi,

thank you for drawing my attention to cell-counter macro. I think I have
found another nice solution to this particular counting problem (see reply
to Bäcker). However, the cell counter macro will be very useful for us in
some of the other work we do.

cheers

anders

> From: Robert Baer <[hidden email]>
> Reply-To: ImageJ Interest Group <[hidden email]>
> Date: Mon, 16 Oct 2006 08:42:27 -0500
> To: <[hidden email]>
> Subject: Re: point selection and counting procedure
>
> You may find Kurt De Vos's cell-counter plugin
> (http://rsb.info.nih.gov/ij/plugins/cell-counter.html) helpful for what you
> are trying to do.  It gives you the possibility of counting and marking
> multiple types of objects in an image.
>
> HTH,
> Rob
>
>
> ----- Original Message -----
> From: "Thorsen, Anders" <[hidden email]>
> To: <[hidden email]>
> Sent: Monday, October 16, 2006 5:53 AM
> Subject: point selection and counting procedure
>
>
>> 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]
>>