Calculating grazing area

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Calculating grazing area

joshcurran
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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Re: Calculating grazing area

Herbie
Good day Josh,

you've realized the main problem with threshold-based binarization...

Although there are equalization methods to help with uneven signals,
they won't do any magic.

Try to find a solution without thresholds:
Perhaps classification may help or a more adequate way of image
acquisition (often not considered!).

In any case, without seeing a _typical_ example image, it is difficult
to give more helpful advice.

Best

Herbie

::::::::::::::::::::::::::::::::::::::::
Am 10.07.17 um 15:53 schrieb joshcurran:

> 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
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Calculating-grazing-area-tp5019047.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Calculating grazing area

PEARSON Matthew
In reply to this post by joshcurran
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



--
View this message in context: http://imagej.1557.x6.nabble.com/Calculating-grazing-area-tp5019047.html
Sent from the ImageJ mailing list archive at Nabble.com<http://Nabble.com>.

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Scotland, with registration number SC005336.

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Re: Calculating grazing area

Glen MacDonald-2
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.


Glen MacDonald
Digital Microscopy Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
depts.washington.edu/digmicro
[hidden email]









> 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
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Calculating-grazing-area-tp5019047.html
> Sent from the ImageJ mailing list archive at Nabble.com<http://Nabble.com>.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Calculating grazing area

Robert Smith
In reply to this post by PEARSON Matthew
Thresholding is based on above and below pixel values, you may have to threshold twice (or more, once above the required limit and once below it.) Yes it is sometimes difficult to cover an irregular area.

Hope this works, it did for me.
Bob

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: PEARSON Matthew<mailto:[hidden email]>
Sent: Monday, July 10, 2017 11:05 AM
To: [hidden email]<mailto:[hidden email]>
Subject: Re: Calculating grazing area

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



--
View this message in context: http://imagej.1557.x6.nabble.com/Calculating-grazing-area-tp5019047.html
Sent from the ImageJ mailing list archive at Nabble.com<http://Nabble.com>.

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Re: Calculating grazing area

jerie
In reply to this post by joshcurran
Dear Josh,

please post an image; your issues with segmentation may result from
illumination artefacts; eg. you would initially try to generate images with
good contrast, because issues during segmentation or classification
oftentimes result from low or uneven contrast.

Kind regards, Jens

Dr. Jens Rietdorf, visiting scientist @ center for technological
development in health CDTS, Oswaldo Cruz Foundation Fiocruz, Rio de Janeiro
Brasil.

On Mon, Jul 10, 2017 at 10:53 AM, joshcurran <[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
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/Calculating-grazing-area-tp5019047.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Jens Rietdorf Visiting Scientist Fundação Oswaldo Cruz - Ministério da Saúde, Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Rio de Janeiro, Brasil.
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