Re: point selection and counting procedure

Posted by Thorsen, Anders on
URL: http://imagej.273.s1.nabble.com/point-selection-and-counting-procedure-tp3701294p3701298.html

Hi,

Thank you for the idea about the ROI manager. I have now found a very good
solution I think: I make a circular ROI that have the diameter of my lower
size threshold. When the particle analysis is fisnished I use the ROI manger
to establish the circlar ROI. I have configured my mouse so that one of the
knobs now works as a "click lock". When I click on the ROI with the click
lock it follows my mouse afterwards. When the ROI is over a cell that is
larger than the ROI I run a "measure and label" macro. I can then continue
to the next cell without any mouse clicking. Another good think about this
is that the data registered from the measure and label command using a
circular ROI is the same data type as from preceding the particle analysis.
This means that all the data can be registred in the same Results window.

thank you!

anders

> From: Volker Bäcker <[hidden email]>
> Reply-To: ImageJ Interest Group <[hidden email]>
> Date: Mon, 16 Oct 2006 13:37:49 +0200
> To: <[hidden email]>
> Subject: Re: point selection and counting procedure
>
> Hi,
> just an idea: Can't you use the Roi Manager to save your point selection?
> You select points. Now you want to measure a distance, so you add your
> point selection to the roi manager. You make the line selection and
> write the
> distance to the results table. Then you restore your point roi from the
> roi manager and you continue to add points (using shift).
> When you finished, you measure the point roi and get your count as the
> number of rows in the results table.
> You could as well put line rois of a specific size into the roi manager
> and use them as reference.
>
> This is more a workaround then a real solution.
> Maybe it would be possible to adapt the new version of the cell counter
> plugin
> http://rsb.info.nih.gov/ij/plugins/cell-counter.html
> to allow for length measurements during the process of counting.
>
> Hope this helps,
> Volker
> Thorsen, Anders a écrit :
>> 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]
>>
>>  
>
> --
> passerelle antivirus du campus CNRS de Montpellier
> --