measuring color in ImageJ

[Melissa Amarello]

Hi,
I am a graduate student studying coloration in a rattlesnake (or I
hope to).  I would like to use ImageJ, with a standardized color card
(X-Rite ColorChecker Card) to estimate reflectance in digital photos.
I have tried using the calibrate function following instructions here:
 http://imagejdocu.tudor.lu/doku.php?id=gui:analyze:calibrate
In greater detail:
I open my jpg image in IJ, which contains the snake whose
color/reflectance I want to measure and the color card
I select an area within each grayscale step on the color card and use
the measure tool to record mean gray values
In "Analyze - Calibrate", I enter the actual mean gray values in the
right column (corresponding to the measured values on the left)
I pick a function (usually polynomial) and click ok.

However, after accepting the calibration function, the image does not
seem to have changed?  I use the color picker to measure color in the
color card and it still says the original, incorrect gray values.
What am I doing wrong?  Is there a better tutorial for the calibrate
function than the one linked above?  Can I use ImageJ to calibrate a
color photo?

thanks,
melissa

Melissa Amarello
National Science Foundation Fellow
Arizona State University (Fall 2009)
http://www.public.asu.edu/~mamarell

[Joachim Wesner]

Hi Melissa,

as far as I can see, the kind of calibration you are refering too in the
link is not about colors at all!
(I.e. about defining what combination of RGB values represent "true gray")

That calibration in the link is about compensating nonlinear detector
behaviour (i.e. a double light intensity
does not read as twice the number) Yes, it will alos not change the image,
but when you read out the pixels
with the cursor, an extra number in brackets should appear that indicates
the calibrated intensity.

What about this plugin ??

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


or Landinis "Color Correct" plugin on that page:

http://www.dentistry.bham.ac.uk/landinig/software/software.html

Cheers

Mit freundlichen Grüßen / Best regards

Joachim Wesner




                                                                           
             Melissa Amarello                                              
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Hi,
I am a graduate student studying coloration in a rattlesnake (or I
hope to).  I would like to use ImageJ, with a standardized color card
(X-Rite ColorChecker Card) to estimate reflectance in digital photos.
I have tried using the calibrate function following instructions here:
 http://imagejdocu.tudor.lu/doku.php?id=gui:analyze:calibrate
In greater detail:
I open my jpg image in IJ, which contains the snake whose
color/reflectance I want to measure and the color card
I select an area within each grayscale step on the color card and use
the measure tool to record mean gray values
In "Analyze - Calibrate", I enter the actual mean gray values in the
right column (corresponding to the measured values on the left)
I pick a function (usually polynomial) and click ok.

However, after accepting the calibration function, the image does not
seem to have changed?  I use the color picker to measure color in the
color card and it still says the original, incorrect gray values.
What am I doing wrong?  Is there a better tutorial for the calibrate
function than the one linked above?  Can I use ImageJ to calibrate a
color photo?

thanks,
melissa

Melissa Amarello
National Science Foundation Fellow
Arizona State University (Fall 2009)
http://www.public.asu.edu/~mamarell



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[Harry Parker]

Hi Melissa,

I believe you are expecting too much from the Calibrate function.
It is designed for grayscale images only.

Also, calibration will not change the image, only the values reported for the pixels.
You could convert your image to grayscale and follow the the instructions again, especially the ones at
http://rsb.info.nih.gov/ij/docs/examples/calibration/

If you want to do true color calibration on images, I suggest checking out other
 programs more focused on color calibration. I like VIPS, with the NIP2 graphical interface.
Here's the main URL:
http://www.vips.ecs.soton.ac.uk/index.php?title=VIPS

Here's the Color Calibration HOW TO page:
http://www.vips.ecs.soton.ac.uk/index.php?title=Colour_calibration_with_nip2

--
Harry Parker
Senior Software Engineer







________________________________
From: Melissa Amarello <[hidden email]>
To: [hidden email]
Sent: Tuesday, August 11, 2009 9:07:06 PM
Subject: measuring color in ImageJ

Hi,
I am a graduate student studying coloration in a rattlesnake (or I
hope to).  I would like to use ImageJ, with a standardized color card
(X-Rite ColorChecker Card) to estimate reflectance in digital photos.
I have tried using the calibrate function following instructions here:
http://imagejdocu.tudor.lu/doku.php?id=gui:analyze:calibrate
In greater detail:
I open my jpg image in IJ, which contains the snake whose
color/reflectance I want to measure and the color card
I select an area within each grayscale step on the color card and use
the measure tool to record mean gray values
In "Analyze - Calibrate", I enter the actual mean gray values in the
right column (corresponding to the measured values on the left)
I pick a function (usually polynomial) and click ok.

However, after accepting the calibration function, the image does not
seem to have changed?  I use the color picker to measure color in the
color card and it still says the original, incorrect gray values.
What am I doing wrong?  Is there a better tutorial for the calibrate
function than the one linked above?  Can I use ImageJ to calibrate a
color photo?

thanks,
melissa

Melissa Amarello
National Science Foundation Fellow
Arizona State University (Fall 2009)
http://www.public.asu.edu/~mamarell