Re: Counting empty circles

Posted by Michael Schmid on Jan 08, 2011; 6:20pm
URL: http://imagej.273.s1.nabble.com/Counting-empty-circles-tp3686043p3686051.html

Hi Scott,

with the exception of the 'refine' button, the Feature Finder plugin can
be called in a macro. You can record the syntax with
Plugins>Macros>Record.

  n = nSlices();
  for (i=1; i<=n; i++) {
    run ("Feature Finder", FeatureFinderOptions);
  }

In case you want a more elaborate function than just 'count' you may also
have a look at the FindStackMaxima macro for an example
  http://rsb.info.nih.gov/ij/macros/FindStackMaxima.txt
(by the way, in the meanwhile the FindStackMaxima macro as such is
obsolete because Find Maxima can process stacks)

Michael
________________________________________________________________


On Fri, January 7, 2011 21:01, Scott Chamberlain wrote:

> Hi Michael,
>
> I wonder if Feature Finder plugin can be automated somehow. I know the
> website says that it does not process stacks, but is there any other way
> to process many images somehow with Feature Finder? I have thousands to
> process.
>
> Thanks! Scott
>
> On Jan 7, 2011, at 5:21 AM, Michael Schmid wrote:
>
>> Hi Scott,
>>
>> you could try my 'Feature Finder' template matching plugin - I have put
>> it online now:
>>  http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:feature_finder:start
>>
>> It seems that the features of interest (trichomes) can appear
>> differently, with or without the bright ring? So you might combine the
>> results obtained with different templates (prototypes).
>> And there are lots of parameters to try: different brightness/contrast
>> of the template, different ROI size in the template, and all the
>> parameters of the dialog box...
>>
>> Michael
>> ________________________________________________________________
>>
>>> Hello,
>>>
>>> I have images (see below) that have many glandular trichomes (the round
>>> shiny objects) which I would like to quantify. I simply want to know
>>> how
>>> many of them there are.  It seems like I should be able to ask ImageJ
>>> to
>>> count the number of these glandular trichomes, but I don't know how to
>>> do
>>> this. I have tried many things already, but have hit a wall. The
>>> smaller
>>> circles within each gland seem to be very consistent in size. I wonder
>>> if
>>> this consistency in size can be used somehow. Thanks so much!
>>>
>>> Sincerely,
>>>
>>> Scott Chamberlain
>>> Rice University, EEB Dept.
>> <Feature_Finder_Test.jpg>
>