Dear Confocalists,
I remind you about Fluorescence 2009 that we are organizing in Mumbai from
March 16-19, 2009. Today is the last date for submitting your abstract.
Though it covers all of "biological fluorescence", there is a heavy presence
of imaging guys in the conference. Check out www.fluorescence2009.org for
the list of speakers. Hope to see you in Mumbai next month.
Sudipta maiti
On Mon, 16 Feb 2009 12:52:00 +1300, Mark Cannell wrote
> As far as Canon is concerned the raw files contain raw sensor data
> as well a lot of other info... Here is a link:
>
> http://lclevy.free.fr/cr2/
>
> Cheers Mark
>
> Chris Tully wrote:
> > Michelle,
> >
> > Not to be to commercial here but the kind of question you are asking
> > here is trivial to answer in most image analysis programs without
> > dropping down to the individual pixel values. Since you are using a
> > single chip color camera keep in mind that some fraction of the pixels
> > in each channel is extrapolated from its neighbors (For a Bayer
> > pattern chip, 75% of the red and blue and 50% or the green pixels are
> > extrapolated from their neighbors!). Assuming that you are talking
> > about "consumer" type digital cameras, I am not as familiar with the
> > chips and filter patterns that they use. Please note that on all the
> > "consumer" grade digital cameras I have used, the "raw" format simply
> > means an uncompressed image (usually in TIFF format). It does not
> > mean the same thing as "raw" means coming from a "scientific" digital
> > camera which usually means a gray scale image exactly as it was
> > extracted from the chip before color processing (interpolation).
> >
> > Taking the software that I am most familiar with as an example
> > (Image-Pro Plus) it is simple, even automatable, to select the range
> > of Red, Green and Blue values of interest and ask the software for
> > anything from the number of objects that meet that threshold to the
> > total number of pixels that meet that threshold. If you have access
> > to a copy of Image-Pro Plus, I would be happy to guide you through the
> > analysis by phone or email.
> >
> > Chris Tully
> > Microscopy and Image Analysis Expert
> > [log in to unmask]
> > 240-888-1021
> > http://www.linkedin.com/in/christully
> >
> >
> >
> > On Fri, Feb 13, 2009 at 11:51 AM, Michelle Peckham
> > <[log in to unmask]> wrote:
> >
> >> 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 [WINDOWS-1252?]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
> >>>>
Dr. Sudipta Maiti
Associate Professor
Dept. of Chemical Sciences
Tata Institute of Fundamental Research
Homi Bhabha Raod, Colaba, Mumbai 400005
Ph. 91-22-2278-2716 / 2539
Fax: 91-22-2280-4610
alternate e-mail: [log in to unmask]
url: www.tifr.res.in/~biophotonics
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