Conifer needle surface area minus shadows

[Tree-Doc]

I have about 250 scans of conifer tree needles and need to measure their
surface area. I've been using Threshold Colour to adjust the HSB to remove
part of the shadow, but I notice that depending on the exact threshold
numbers I use, my resulting area calculation will vary by 25% or more (not
good).

Is there a better way to do this to achieve more accurate results?

My methods: Adjust HSB to remove as much of the shadow as I can without
removing green needle.
Converting to binary.
Despeckling the noise.
Process>Binary>Close to capture the white center streaks in the needles.
Filling the Holes.
And analyzing particles

Here is an example of the images I'm working with. I know the scans aren't
ideal, but capturing better images in not an option.

[Shameem Sampath]

Hi Tree-Doc,
I have a suggestion. Please accept my apologies if you have already explored this avenue :
 (a) Take a pic using a polarising filter to reduce the reflected glare.
(b). Follow the pathway you have described.

Kind regards,
Shameem Sampath MD
Consultant Knee Surgeon
The Bluespot Knee Clinic
Manchester
England
www.MrSampath.com



Sent from my iPhone

> On 8 Dec 2013, at 23:03, Tree-Doc <[hidden email]> wrote:
>
> I have about 250 scans of conifer tree needles and need to measure their
> surface area. I've been using Threshold Colour to adjust the HSB to remove
> part of the shadow, but I notice that depending on the exact threshold
> numbers I use, my resulting area calculation will vary by 25% or more (not
> good).
>
> Is there a better way to do this to achieve more accurate results?
>
> My methods: Adjust HSB to remove as much of the shadow as I can without
> removing green needle.
> Converting to binary.
> Despeckling the noise.
> Process>Binary>Close to capture the white center streaks in the needles.
> Filling the Holes.
> And analyzing particles
>
> Here is an example of the images I'm working with. I know the scans aren't
> ideal, but capturing better images in not an option.
> <http://imagej.1557.x6.nabble.com/file/n5005845/4L0001_exp.jpg>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Conifer-needle-surface-area-minus-shadows-tp5005845.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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[Michael Sarahan]

How do you determine your thresholds?  If you can come up with some
formula, rather than doing it by eye, that's probably a good start.  Of
course, I'm then assuming that you have a reasonably well-controlled image
acquisition system.  Are you using the same scanner every time?  Does it do
any kind of auto-adjustment?  You probably want to disable that, so that it
gives you the same imaging conditions every time (even if they're not
always as nice as they might be).

Once you come up with "standard" values for the threshold, you could
perhaps establish the systematic error that your standard values introduce
by manually measuring things on one image, and come up with some correction
factor to use on the rest of the images.

HTH,
Mike


On Sun, Dec 8, 2013 at 7:02 PM, Shameem Sampath
<[hidden email]>wrote:

> Hi Tree-Doc,
> I have a suggestion. Please accept my apologies if you have already
> explored this avenue :
>  (a) Take a pic using a polarising filter to reduce the reflected glare.
> (b). Follow the pathway you have described.
>
> Kind regards,
> Shameem Sampath MD
> Consultant Knee Surgeon
> The Bluespot Knee Clinic
> Manchester
> England
> www.MrSampath.com
>
>
>
> Sent from my iPhone
>
> > On 8 Dec 2013, at 23:03, Tree-Doc <[hidden email]> wrote:
> >
> > I have about 250 scans of conifer tree needles and need to measure their
> > surface area. I've been using Threshold Colour to adjust the HSB to
> remove
> > part of the shadow, but I notice that depending on the exact threshold
> > numbers I use, my resulting area calculation will vary by 25% or more
> (not
> > good).
> >
> > Is there a better way to do this to achieve more accurate results?
> >
> > My methods: Adjust HSB to remove as much of the shadow as I can without
> > removing green needle.
> > Converting to binary.
> > Despeckling the noise.
> > Process>Binary>Close to capture the white center streaks in the needles.
> > Filling the Holes.
> > And analyzing particles
> >
> > Here is an example of the images I'm working with. I know the scans
> aren't
> > ideal, but capturing better images in not an option.
> > <http://imagej.1557.x6.nabble.com/file/n5005845/4L0001_exp.jpg>
> >
> >
> >
> > --
> > View this message in context:
> http://imagej.1557.x6.nabble.com/Conifer-needle-surface-area-minus-shadows-tp5005845.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
>

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[Oky]

Hello,

With the previous good suggestions, if you use no cover with your scanner
when you scan the samples, the scanned image will have black background but
your needles have no shadows.  It looks like dark field micrographs.

I used this trick when I measure surface areas of 20 wood blocks at one
scan. Also it is going to be much easier to apply automatic threshold for
the needles.

One thing you should be aware of images of samples. When the samples are
located away from the scan axis (center part of the scanner along scan head
movement) of your scanner will have side view. That might affect
significant influence on the surface area that you want to measure
depending on shape of your samples.

I hope this helps you make measurement easier and more accurate.

Best regards,

Ohkyung




On Mon, Dec 9, 2013 at 8:03 AM, Tree-Doc <[hidden email]> wrote:

> I have about 250 scans of conifer tree needles and need to measure their
> surface area. I've been using Threshold Colour to adjust the HSB to remove
> part of the shadow, but I notice that depending on the exact threshold
> numbers I use, my resulting area calculation will vary by 25% or more (not
> good).
>
> Is there a better way to do this to achieve more accurate results?
>
> My methods: Adjust HSB to remove as much of the shadow as I can without
> removing green needle.
> Converting to binary.
> Despeckling the noise.
> Process>Binary>Close to capture the white center streaks in the needles.
> Filling the Holes.
> And analyzing particles
>
> Here is an example of the images I'm working with. I know the scans aren't
> ideal, but capturing better images in not an option.
> <http://imagej.1557.x6.nabble.com/file/n5005845/4L0001_exp.jpg>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Conifer-needle-surface-area-minus-shadows-tp5005845.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ohkyung Kwon

http://nicem.snu.ac.kr
http://www.linkedin.com/in/ohkyung
http://www.wpskorea.org

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[Cheng Zhang]

Equalization filter may also work.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Shameem Sampath
Sent: December 8, 2013 20:02
To: [hidden email]
Subject: Re: Conifer needle surface area minus shadows

Hi Tree-Doc,
I have a suggestion. Please accept my apologies if you have already explored this avenue :
 (a) Take a pic using a polarising filter to reduce the reflected glare.
(b). Follow the pathway you have described.

Kind regards,
Shameem Sampath MD
Consultant Knee Surgeon
The Bluespot Knee Clinic
Manchester
England
www.MrSampath.com



Sent from my iPhone

> On 8 Dec 2013, at 23:03, Tree-Doc <[hidden email]> wrote:
>
> I have about 250 scans of conifer tree needles and need to measure their
> surface area. I've been using Threshold Colour to adjust the HSB to remove
> part of the shadow, but I notice that depending on the exact threshold
> numbers I use, my resulting area calculation will vary by 25% or more (not
> good).
>
> Is there a better way to do this to achieve more accurate results?
>
> My methods: Adjust HSB to remove as much of the shadow as I can without
> removing green needle.
> Converting to binary.
> Despeckling the noise.
> Process>Binary>Close to capture the white center streaks in the needles.
> Filling the Holes.
> And analyzing particles
>
> Here is an example of the images I'm working with. I know the scans aren't
> ideal, but capturing better images in not an option.
> <http://imagej.1557.x6.nabble.com/file/n5005845/4L0001_exp.jpg>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Conifer-needle-surface-area-minus-shadows-tp5005845.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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