Re: Cell counting with imageJ

Posted by Gabriel Landini on
URL: http://imagej.273.s1.nabble.com/Cell-counting-with-imageJ-tp3690375p3690376.html

On Friday 20 November 2009, Lukas Hoffmann wrote:
> My basic idea is, you count a few images by hand and tell the program what
> the count "should" be.  Then the program changes the way it does the
> thresholding & image processing in many different ways, and
> compares all of its test counts with the correct count.  When the
> program finds one type of image processing that has a low error rate
> compared to the manual counting, it uses that type of processing for
> the rest of your images.

The problem with that approach is that it is counting objects without
knowing whether they are the same in the gold-standard count and in the test
count.

If you have 10 objects (each one is a cell) in the gold standard and only 1 of
those cells is recognised in the test image, but the cell is fragmented by the
segmentation procedure in 10 pieces, you would be assuming that the program is
counting perfectly when it is not.

Counts alone is not enough. You need to know that the segmented blobs somewhat
match (in position, size, shape) the gold standard blobs, only then you could
count them, but otherwise the assumption that they are the same in both images
is not satisfied.

Regards

G.