Quantifying red colouration in ImageJ

[amelia176]

Hi,

part of my current research includes having to quantify the colour red in male sticklebacks. I will be taking photos of the side of the fish and will be using a colour checker chart to standardise the images. Is there a way for me to calibrate the red on the colour chart as true red and then quantify redness in ImageJ?

If not, is there any other software where I can do this? I see lots of people have used the L*A*B function in photoshop?

thanks,

Amelia

[Christian Liebig-3]

Hi,

I assume you are taking RGB  images. They can basically be seen as a
3-channel spectral dataset. So you could define the "spectrum" for the
red area on the chart as a reference spectrum and then check how well
your fish's red "spectrum" correlates to that. You can download a set of
macros for doing that here
<https://owncloud.tuebingen.mpg.de/public.php?service=files&t=dc469fba54ddb758f04229c83e44ea82>.

If you need any help in setting up the workflow please let me know.

Best,
Christian


On 20.03.2016 19:02, amelia176 wrote:

> Hi,
>
> part of my current research includes having to quantify the colour red in
> male sticklebacks. I will be taking photos of the side of the fish and will
> be using a colour checker chart to standardise the images. Is there a way
> for me to calibrate the red on the colour chart as true red and then
> quantify redness in ImageJ?
>
> If not, is there any other software where I can do this? I see lots of
> people have used the L*A*B function in photoshop?
>
> thanks,
>
> Amelia
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Quantifying-red-colouration-in-ImageJ-tp5015956.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Christian Liebig, PhD

Light Microscopy Facility
Max-Planck-Institute for Developmental Biology
Spemannstrasse 35
D-72076 Tuebingen
Germany

Phone:  [phone]
e-mail: [hidden email]


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[Peter Haub]

Hallo Amelia,

color quantification is discussed in various (industrial and) biological
applications since along time. Depending on the accuracy requirements
color calibration and measurement can be very complex and difficile.

Assuming you have a homogeneous and spectrally stable illumination you
could - as a first trial - simply compare the values of the red image
channel of your samples in reference to either a red sample of a color
chart or more simply to a white reflection standard. (use the IJ
function Image / Color / Split Channel)

The 'red value' can be seen as a measurement of the integrated light
intensity in the 'red spectrum' of your camera (see the spectral sensor
characteristics of your camera data sheet). Of course you should work
with fixed camera settings such as gain, white calibration, integration
time etc.

If you are using a color camera with a Bayer mosaic filter you should
try to work with the camera RAW data if your camera offer this option.

Maybe it is also an option for you to add a small banded color filter
into the optical path to narrow the 'red spectrum'. In this way you
increase the specificity of your measurement.


Some helpful hints and information regarding color measurement can be
found in

https://en.wikipedia.org/wiki/Color_difference

http://www.brucelindbloom.com/

http://imagej.1557.x6.nabble.com/Color-Quantification-or-counting-td3695993.html




On 20.03.2016 19:02, amelia176 wrote:

> Hi,
>
> part of my current research includes having to quantify the colour red in
> male sticklebacks. I will be taking photos of the side of the fish and will
> be using a colour checker chart to standardise the images. Is there a way
> for me to calibrate the red on the colour chart as true red and then
> quantify redness in ImageJ?
>
> If not, is there any other software where I can do this? I see lots of
> people have used the L*A*B function in photoshop?
>
> thanks,
>
> Amelia
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Quantifying-red-colouration-in-ImageJ-tp5015956.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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Gabriel Landini]

On 20.03.2016 19:02, amelia176 wrote:
> part of my current research includes having to quantify the colour red in
> male sticklebacks. I will be taking photos of the side of the fish and
> will be using a colour checker chart to standardise the images. Is there a
> way  for me to calibrate the red on the colour chart as true red and then
> quantify redness in ImageJ?

See here, it might be useful.

http://imagejdocu.tudor.lu/doku.php?id=plugin:color:chart_white_balance:start

Cheers

Gabriel

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[JRGOMES]

 

Hello Dear colleagues .

Someone could help me, sending to me a tutorial, please?

I need to measure the quantities de fiber of collagen I and III from of
the Picrossirius staining.

use the 1967jrgomes@gmail please.

Sincerely

---
Jose

Em 21/03/2016 12:01, Gabriel Landini escreveu:

> On 20.03.2016 19:02, amelia176 wrote:
>
>> part of my current research includes having to quantify the colour red in male sticklebacks. I will be taking photos of the side of the fish and will be using a colour checker chart to standardise the images. Is there a way for me to calibrate the red on the colour chart as true red and then quantify redness in ImageJ?
>
> See here, it might be useful.
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:color:chart_white_balance:start [1]
>
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html [2]

 

Links:
------
[1]
http://imagejdocu.tudor.lu/doku.php?id=plugin:color:chart_white_balance:start
[2] http://imagej.nih.gov/ij/list.html

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