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thresholding and detection issues when analyzing particles to obtain object counts in a petri dish

Posted by Rich Pendleton on Dec 08, 2015; 8:57pm
URL: http://imagej.273.s1.nabble.com/thresholding-and-detection-issues-when-analyzing-particles-to-obtain-object-counts-in-a-petri-dish-tp5015178.html

Hey all,



I was wondering if someone might be able to provide some insight similar to
a question that was posted last month.  I am trying to use the analyze
particles function to count fish eggs in a petri dish.  Some eggs are more
mature than others and the smaller less mature eggs are rather
transparent.  Therefore when trying to adjust the threshold to detect the
less mature eggs, I get clumping of mature eggs that are in close proximity
to one another.  Despite using the watershed function in attempt to
separate eggs that are close, I still have many large clumps that have
numerous eggs that are being counted as one unit. As a result, the counts
are always much less than the true count (often over 1000 eggs less). If I
adjust the threshold in the other direction, I am unable to detect the less
mature eggs.  It is quite difficult to prevent eggs from clumping when the
petri dish is first scanned therefore was hoping I might be able to get
around it within ImageJ. I have attached a few pictures (from top to
bottom) 1) original image set to 8 bit, 2) after thresholding, 3) after
watershed, 4) outlines of counted particles.  The original image was
scanned in as a jpeg with 1200 dpi.  Any help that you may be able to
provide would be greatly appreciated.



Cheers,



Rich Pendleton

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8bit (Copy).jpg (74K) Download Attachment
outlines (Copy).jpg (52K) Download Attachment
threshold (Copy).jpg (100K) Download Attachment
watershed (Copy).jpg (95K) Download Attachment