CONFOCALMICROSCOPY Archives

February 2009

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Subject:
From:
Michelle Peckham <[log in to unmask]>
Reply To:
Confocal Microscopy List <[log in to unmask]>
Date:
Fri, 13 Feb 2009 16:51:27 +0000
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Thanks Jerry

These are pictures taken with a digital camera (i.e. Nikon or Canon) in
'raw' format. So your advice is great.

This person wants to work out how much area is a particular shade/hue, so we
thought grey scale numbers in R,G and B channels would be the thing to go
for.

So thanks for this.

Michelle


On 13/02/2009 16:46, "Jerry Sedgewick" <[log in to unmask]> wrote:

> Is the file in the Raw format, such as those generated by Nikon and
> Canon consumer cameras? Or did you mean that the person was asking about
> the original (unaltered or raw) file?
> 
> If it is the Nikon or Canon Raw format, then it was derived from a
> mosaic chip and colors will have to be assigned to each pixel through
> some kind of conversion "engine." Photoshop uses its own Adobe Camera
> Raw (ACR) engine in all the CS versions (as I recall). If the lighting
> for the study was consistent, and if the study occurred over more than
> one imaging session, then the settings in Adobe Camera Raw should be set
> similarly for the experiment, or the colors will have to be adjusted by
> using a reference standard (such as a neutral gray card, Macbeth color
> chart, or some consistent part of the specimen that is white or gray).
> If the colors are not assigned or adjusted to a standard, then the
> colors will be inconsistent from session to session.
> 
> Canon and Nikon both have proprietary engines in which colors are
> generated at each x, y position. These can also be used, but make sure
> the gamma is set to 1, and, again, adjust colors based upon reference
> standards if images were taken at more than one session.
> 
> Before opening the image in Photoshop, the Color Settings in the menu
> (Preferences>Color Settings) are changed from the RGB default setting
> (sRGB....). A "CIE 1931 D65" setting is chosen because this keeps the
> gamma at 1 (no alteration of post-ACR values). This color setting can be
> downloaded from quickphotoshop.com, but make sure to click on Book:
> Supplemental Info (not Download). Photoshop changes the gamma when using
> any of the other color settings. Gamma is a reference to the adjustment
> of pixel values destined for display on a computer monitor in which the
> Greek symbol gamma is the exponent in a math formula.
> 
> Once in Photoshop, in the menu, under Windows, choose Channels
> (Windows>Channels). In the Channels palette, click on the upper right
> arrowhead and choose Split Channels from the drop down list. This will
> separate the red, green and blue channels for subsequent measurement.
> 
> In the distant past, I believe I used Image J to generate pixel values
> at each x, y position, but maybe it was MatLab or MetaMorph. Maybe
> another person on the list can add that information.
> 
> Cheers!
> 
> 
> 
> Michelle Peckham wrote:
>> A little bit off the topic, but
>> 
>> Someone here was asking me about analysing a ŚRAWą file for colour
>> information, and the simplest way to do what she wants would be to
>> extract the grey scale values out for the red, green and blue
>> channels, and analyse them in a spread sheet.
>> 
>> Does anyone know how to do this?
>> 
>> Michelle 
> 

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