http://imagej.273.s1.nabble.com/Calculating-grazing-area-tp5019047p5019050.html
Since the images are apparently captured in color, splitting the channels may provide one channel with better contrast between grazed and ungrazed areas. Or each channel does a better job with a different region which would allow you to threshold each and add them together. Of course, if your images are in JPEG format, color and resolution are compromised. Another option is to add another form of contrast, such as Hoffman, DIC, darkfield or simply close down the condenser diaphragm for a compound microscope, try oblique lighting with a dissecting ‘scope.
> On Jul 10, 2017, at 8:01 AM, PEARSON Matthew <
[hidden email]> wrote:
>
> Hi Josh,
>
> Well I didn't think i'd be discussing snails today! :) Sometimes you can use morphological filters to pre-process the image which I find sometimes improves the accuracy of thresholding, see the Process menu. I guess you could also try manually drawing around the grazing area using a selection tool and subtract this from the total image area-could be laborious but hard to know without an image as herbie says. For example i'm assuming this is a black and white image from a microscope using transmitted brightfield or some kind of episcopic illumination?
>
> Thanks,
>
> Matt
>
> --
> Matt Pearson
> Microscopy Facility
> MRC Human Genetics Unit
> Institute of Genetics and Molecular Medicine (IGMM)
> University of Edinburgh
> Crewe Road
> EH4 2XU
>
>
>
>
> On 10 Jul 2017, at 14:53, joshcurran <
[hidden email]<mailto:
[hidden email]>> wrote:
>
> Hi there,
>
> I'm brand new to ImageJ and am just trying to get to grips with it. I've
> been playing around with it all day.
>
> I'd like to calculate the percentage area grazed by snails across an algal
> biofilm. I understand that I can threshold the image, but the biofilm isn't
> amazingly consistent with colour across the dish. When I was practicing and
> testing it out earlier on when thresholding it wasn't really covering the
> parts I wanted it to. Any advice or tips? Or is there another way that
> grazing area could be measure?
>
> Many thanks,
> Josh
>
>
>
> --
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