Re: Analyse particles: counting eggs query

Posted by Amy Mikhail on Sep 19, 2005; 8:27pm
URL: http://imagej.273.s1.nabble.com/Analyse-particles-counting-eggs-query-tp3704847p3704848.html

Hi all,

Thanks for all the replies, watershed and euclidian distance was a good
tip ... however I'm also interested in some of the suggestions below
(which I guess touch on similar points);

(a) How would I go about putting my formula in the ImagJ results table as
suggested by JiHo(I'm not a computer programmer, so don't know any Java
but willing to give it a try with some explicit instructions!)

(b)How would I get batch processing to work (Chris)?

Thanks again,

Amy.


> I guess that what you will probably do (if watersheding doesn't solve
> the problem) is to modify the particle analysis plugin and introduce
> a new collum in the results table which is the output of your
> formula. It is not difficult to code it in Java (really, I mean it!)
> and you'll spare you the use of nasty proprietary softwares. ;-)

> JiHO

> OK, first of all, check out Excel_Writer at
> http://rsb.info.nih.gov/ij/plugins/excel-writer.html to automatically
> import your results to an Excel spreadsheet.  You should be able to
count your eggs if they are not too clumped using some variant of the
binary processing Euclidean Distance Map either Ultimate Points or
Watershed segmentation to separate your touching eggs.  However,
division by the egg size may also be satisfactory for your purposes.
There are some errors in any approach you take, but you should be able
to deal with them.
>
> Also, you can do your math right in ImageJ before exporting to Excel if
> you want.  Also, if you have lots of images, you can batch process them,
> thereby automating the whole process and limited only by your hard drive
capacity. Let me know if you need pointers for any or all of these
procedures.

> Chris Coulon



----------------------------------------------------------------------------

>> Hello all,
>>
>> I've recently been using the image J "analyse", "analyse particles"
>> function to count mosquito eggs (digital photo taken of black eggs on
>> white filter paper).
>>
>> One difficulty is that the eggs tend to stick to each other, and often
>> appear lying side by side.  In this instance, Imaje J counts all the
>> eggs
>> that are not separate as one.
>>
>> Manually separating the eggs out without damaging them is quite
>> difficult
>> and very time consuming.  Luckily the eggs do not vary much in size , so
>> to overcome this problem, I have worked out the size range (in pixels)
>> of
>> an average single egg (9 - 22 pixels).  I carry out 3 counts:
>>
>> 1. < 9 pixels
>> 2. 9-22 pixles
>> 3. > 22 pixels
>>
>> Particles counted in the first range are too small to be eggs and are
>> probably dust / artifacts (large artefacts are removed from the photo
>> prior to processing).  Particles in the second range are all the eggs
>> that
>> have been counted singly, while particles in the 3rd range are eggs that
>> are stuck together and have been counted incorrectly.  To get a total
>> (more accurate) count,  I use this formula:
>>
>> Range 2 Count + (Range 3 total area / range 2 mean particle area).
>>
>> (Areas are in pixels - means are taken from each photo to account for
>> differences in zoom etc)
>>
>> So here is my query; currently I am using an excel sheet to compute the
>> formula - I add the necessary results from Image J manually to the excel
>> sheet.  Would it be possible to feed the Image J results I need directly
>> into the excel sheet?  If so how would I do this?
>>
>> BTW we are trying to set up this system to use in experiments where
>> large
>> numbers of egg papers will be processed on a daily basis (by various
>> people).  Using image J as opposed to counting manually is already a
>> vast
>> improvement (both time-wise and in terms of human error), so what I'm
>> after is a bit of fine tuning to further expedite the process.
>>
>> Any advice / help on this would be greatly appreciated...
>

-------------------------------------------
Amy Mikhail
Research student
University of Aberdeen
Zoology Building
Tillydrone Avenue
Aberdeen AB24 2TZ
Scotland
Email: [hidden email]
Phone: [phone] (lab)