Densitometry (or relative optical density)

Discussion in 'Photoshop Tutorials' started by Jason Wong, Aug 1, 2003.

  1. Jason Wong

    Jason Wong Guest

    Hi, I'm trying to figure out how to use Photoshop for scientific image
    analysis purposes. I'm doing some neuroscience research, and what I
    need to analyze is the intensity in certain brain regions created by a
    specific staining technique. So what I was thinking of doing is using
    the square marquee of Fixed Size to anaylze a square from Region A, and
    compare that to a same area in Region B. What confuses me the most is
    if I do Image --> Histogram, the value for Mean seems to be inversly
    proportional to the staining intensity. i.e., if the region is darkly
    stained I get a small Mean value and vice versa.

    Does anyone know what I'm talking about? Is there a specific formula I
    would use in order to determin the relative optical density of a certain
    region? Any help would be greatly appreciated!

    -- Jason
    Jason Wong, Aug 1, 2003
    #1
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  2. John Stafford, Aug 1, 2003
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  3. Jason Wong

    Mike Russell Guest

    Don wrote:
    > The number you are reading is the brightness of the spot from 0-255,
    > not the density. The density in absolute terms is therefore
    > porportional to the inverse of the number, or in density numbers to
    > the log(10) of the inverse of the number/255.


    Correct. Also, don't forget gamma. This is an exponential funciton applied
    to the data before it is displayed. In practical terms this means an image
    value of 128 will be somewhat darker than 50% intensty.

    You may set a custom working space with a gamma of 1.0 to eliminate this.

    --

    Mike Russell
    http://www.curvemeister.com
    http://www.zocalo.net/~mgr
    http://geigy.2y.net
    Mike Russell, Aug 1, 2003
    #3
  4. Jason Wong

    Jason Wong Guest

    Well Fovea Pro sounds like a great program but at $800 I don't think I
    can afford it! Is there no other way to do this manually? Like as
    someone said before can I take the log of the intensity to get
    density?
    Jason Wong, Aug 2, 2003
    #4
  5. "Jason Wong" <> wrote in message
    news:...
    > Well Fovea Pro sounds like a great program but at $800 I don't think I
    > can afford it! Is there no other way to do this manually? Like as
    > someone said before can I take the log of the intensity to get
    > density?


    Photoshop unfortunately only reports in 8-bit/channel values, even for (15
    or) 16-b/ch values. So you are limited to a relative (to the brightest
    pixel) Optical Density range of 0.0-2.4 . If that is enough for your
    purpose, there seems to be no other way than calculating by hand, or using a
    look-up table. As mentioned, make sure the image data is in Gamma 1 space.

    Maybe, I'm not sure because my trial period expired, Picture Window (Pro for
    16-b/ch) has such a functionality? Check http://www.dl-c.com for details.

    Bart
    Bart van der Wolf, Aug 2, 2003
    #5
  6. Jason Wong <> wrote:

    >Hi, I'm trying to figure out how to use Photoshop
    >for scientific image analysis purposes.


    Photoshop has some "enhancements" that makes it is rather difficult to
    utilize it for scientific purposes.

    >I need to analyze is the intensity in certain brain
    >regions created by a specific staining technique.


    What is it that gives the "intensities"? X-ray film or something else?


    >I was thinking of doing is using the square marquee
    >of Fixed Size to anaylze a square from Region A, and
    >compare that to a same area in Region B. What confuses
    >me the most is if I do Image --> Histogram, the value
    >for Mean seems to be inversly proportional to the
    >staining intensity.


    The relation depends on the working-space gamma, among other things.

    >i.e., if the region is darkly stained I
    >get a small Mean value and vice versa.


    Yes, the relative whitepoint is RGB=255,255,255, from there on it gets
    darker and darker as you approach to level RGB=0,0,0.

    >Is there a specific formula I would use in order
    >to determin the relative optical density of a
    >certain region?


    Yes there is but one needs to know what the source is, it has to have a
    known relation to density in the first place.

    Timo Autiokari http://www.aim-dtp.net
    Timo Autiokari, Aug 3, 2003
    #6
  7. Jason Wong

    Tom Nelson Guest

    In article <SPvXa.63741$uu5.6238@sccrnsc04>, Leonard Evens
    <> wrote:

    > Photoshop starts with values in the range 0..255 (for each channel)
    > obtained from some source. That source could be a digital camera or
    > more likely in your case a scanner used to scan the Xray film. One
    > would have to know just what that device is doing in creating the values
    > 0..255. For example, Vuescan used in conjunction with one of the
    > standard film scanners can actually show what Ed Hamrick tells us is the
    > density of the film at each point in the scan. I haven't checked
    > with a densitometer to see if his values are accurate, but they
    > certainly seem to be in the right ball park of what I would expect. But
    > his software, as does any scanning software, converts the density values
    > to RGB values in the range 0..255. How it does it depends on some
    > parameters, including the white and black points and a value of gamma.
    > Since the aim in scanning is to get a usable image, whatever the density
    > range in the source, it is going to be difficult to relate the latter
    > values to density.


    Most scanning software allows you to save scanning parameters. Might
    you prepare a slide with the maximum possible stain next to an
    unstained area? You could relate those densities to 0 and 255,
    respectively, and use that setting for your test slides.
    Tom Nelson
    Tom Nelson Photography
    Tom Nelson, Aug 4, 2003
    #7
  8. Jason Wong

    Mike Russell Guest

    > Jason Wong wrote:
    >> Hi, I'm trying to figure out how to use Photoshop for scientific
    >> image analysis purposes. I'm doing some neuroscience research, and
    >> what I need to analyze is the intensity in certain brain regions
    >> created by a specific staining technique. So what I was thinking of
    >> doing is using the square marquee of Fixed Size to anaylze a square
    >> from Region A, and compare that to a same area in Region B. What
    >> confuses me the most is if I do Image --> Histogram, the value for
    >> Mean seems to be inversly proportional to the staining intensity.
    >> i.e., if the region is darkly stained I get a small Mean value and
    >> vice versa.
    >>
    >> Does anyone know what I'm talking about? Is there a specific
    >> formula I would use in order to determin the relative optical
    >> density of a certain region? Any help would be greatly appreciated!


    I've been thinking some more about this.

    Most, if not all, of the replies to your question have concentrated on the
    numeric conversion of RGB values to density. This response is centered on
    your need to calculate the average density of a selected area, thereby
    getting the value of the total amount of stain absorbed by a particular area
    of a cell.

    Density is minus the log of the fraction of transmitted light, aka
    transparency. For example, clear film would have a transparencyof 1.0 and a
    density of -log(1.0) = 0.0. An area of film that transmits 1/100 of the
    light would have a density of -log(.01) = 2.0.

    In black and white film density is proportional to the mass of silver per
    unit area, and this corresponds to your goal of measuring the mass of stain
    absorbed in a particular area of the cell. I cannot think of an exact way
    to do this in Photoshop because it deals in luminance directly, and not the
    log of luminance.

    1) avoid gamma issues by converting the image to Lab mode.

    2) You will need to calibrate the luminance values by matching a couple of
    density points, using using a specimen with known density values. This
    amounts to subtracting the background density from your measurements, and
    scaling to match a maximum density. Once this is done, you may read
    luminance values from your 50% means a 50% tranaparency value, or a density
    of -log(.5) = .30

    3) selecting an area with the lasso will .cause Image>Histogram to display
    the average percent lightness of that area.

    4) Subtracting that number from 100 and taking the log will give you an
    accurate density only if the stain for that area is uniform. If there is
    much variation in density, the result will be only an approximate average
    density.

    Unfortunately, at the end of the day, the density number yielded by this
    method is based on an average transparency, and not an average density.

    The problem with that is this. Consider a stained area consisting of a
    checkerboard of .1 and 1.0 transparency , corresponding to density values of
    1.0 and 0.0, respectively. The average transparency will be .55, and the
    density calculated from this would be -log(.55) = .25, and not the correct
    value of .5. If your subject does not vary much in density, the numbers
    just might be accurate enough using this method. My guess is not.

    One solution to this is to save the image as a 16 bit grayscale (the raw
    file format is probably easiest to deal with), and write a C or Visual Basic
    program to take the logs. You may then open this image in Photoshop, and
    use the histogram tool to measure density values directly.

    Another solution would be to have a custom plugin written to do this
    calculation. If this is a university setting, and you have student cycles
    available this could be very reasonable solution to your problem. Or hire a
    summer student.

    There is also a Macintosh only program called NIH image that will do a
    variety of quantitative measurements of images:
    see <http://rsb.info.nih.gov/nih-image/>


    --

    Mike Russell
    http://www.curvemeister.com
    http://www.zocalo.net/~mgr
    http://geigy.2y.net
    Mike Russell, Aug 4, 2003
    #8
  9. Jason Wong

    Jason Wong Guest

    Thanks everyone for the helpful replies. However I'm still a little
    befuddled and confused as to what to do... I've switched to trying to
    learn ImageJ, a java based image analysis program which is the PC
    version of NIH Image (produced by the National Institute of Health).
    But I think I'm back to where I started, basically I don't think I can
    convert my mean values to density without some kind of calibration
    step tablet or something like that. Here's a copy of the message I
    just wrote to two other forums for help with ImageJ. Hopefully this
    will clear up what I wanted to do and maybe someone can tell me how to
    do it (easily preferrably!) in either photoshop or ImageJ. Thanks!

    ----

    Hello, I'm trying to analyze hippocampal brain slices which I have
    been immunostained for a neuronal marker (SNAP-25). All areas of the
    slice in which synaptic connections are occurring are stained brown,
    so the only unstained areas are where no tissue exists or where cell
    bodies are located. The hippocampus is composed of several regions of
    different neuron types (e.g. CA1, CA3, dentate gyrus), which are
    clearly demarked using this stain by differential staining
    intensities. However due to difficulties with the staining protocol,
    staining intensities were not uniform from day to day, brain to brain,
    and even parallel slice to slice. So to normalize this, I'm going to
    be dealing with ratios between one hippocampal region and another.

    So far I've converted my RGB images to 8-bit grayscale by selecting
    Image -> Type -> 8-bit. I then openned up an image of a scale bar
    used to set the scale by selecting Analyze -> Set Scale. Next I drew
    a rectangle area selection tool to draw a square of fixed area (88
    squared pixels). I then moved the square to the CA1 region, and
    recorded the mean gray value by selecting Analyze -> Measure. Finally
    I moved the selection square to record the mean gray value for a total
    of 3 regions per image.

    What I'm mostly confused with is what the mean gray value actually
    MEANS. For the darker regions, I get a lower mean value but for the
    lighter regions, I get a greater one. That seems to go against what I
    would think of intuitively of what I actually want -- which is pixel
    density. So if region A is darker than region C, I'd get a larger
    value for region A. Final analysis would involve taking the ration of
    A to C and comparing it with another region, such as B to C.

    Someone mentioned something about calibrating my images. I'm not too
    sure what this means or entails, but I don't think I have access to a
    calibrated optical density step tablet. I don't know if that would
    help either because each image I took might have slight changes in
    brightness as I often fiddled around with the imaging system to
    produce the best "looking" picture. But I figure the ratios idea will
    help solve that dilema.

    If anyone can understand what I'm trying to do and give me some help,
    please please please do! Thank you
    Jason Wong, Aug 11, 2003
    #9
  10. "Jason Wong" <> wrote in message
    news:...
    SNIPped introduction
    > So far I've converted my RGB images to 8-bit grayscale by selecting
    > Image -> Type -> 8-bit. I then openned up an image of a scale bar
    > used to set the scale by selecting Analyze -> Set Scale. Next I drew
    > a rectangle area selection tool to draw a square of fixed area (88
    > squared pixels). I then moved the square to the CA1 region, and
    > recorded the mean gray value by selecting Analyze -> Measure. Finally
    > I moved the selection square to record the mean gray value for a total
    > of 3 regions per image.


    Okay, you have now RGB Gray values. As far as I can see, all ImageJ (just
    like
    Photoshop) does when you convert to 8-bit is take the unweighted average or
    mean (R+G+B)/3. These RGB values are a sort of brightness (higher values are
    brighter) on a scale from 0 to 255.

    > What I'm mostly confused with is what the mean gray value actually
    > MEANS. For the darker regions, I get a lower mean value but for the
    > lighter regions, I get a greater one. That seems to go against what I
    > would think of intuitively of what I actually want -- which is pixel
    > density. So if region A is darker than region C, I'd get a larger
    > value for region A. Final analysis would involve taking the ration of
    > A to C and comparing it with another region, such as B to C.


    You seem to be looking for Optical Density values, which would then be
    calculated as D=Log10(255/measured), assuming the brightest value in the
    image equals 255. This would give higher density values for darker tones, on
    a logarithmic scale, and the difference of two values in Log space is the
    same as a ratio in Linear space.

    > Someone mentioned something about calibrating my images. I'm not too
    > sure what this means or entails, but I don't think I have access to a
    > calibrated optical density step tablet.


    The best you can do with the above approach, is Relative density and not
    Absolute density. Relative density to a lightest measurement of 255 only
    gives a range of 2.4 density but that may be enough for your purpose.
    Because you only have 255 logarithmicly spaced values you will create gaps
    in the range at one end, and loss of precision at the other. Calibration
    only offers to get Absolute density instead of Relative density.

    Hope that helps a bit.

    Bart
    Bart van der Wolf, Aug 11, 2003
    #10
  11. Jason Wong

    DrJohnRuss Guest

    "Bart van der Wolf" wrote

    .... big snip...

    >You seem to be looking for Optical Density values, which would then be
    >calculated as D=Log10(255/measured), assuming the brightest value in the
    >image equals 255. This would give higher density values for darker tones, on
    >a logarithmic scale, and the difference of two values in Log space is the
    >same as a ratio in Linear space.


    That's not really good enough. Bart is assuming that your recorded 0..255
    values represent a linear measure of the original transmitted light. That
    probably isn't true. It certainly isn't true if the original RGB image was
    captured with a typical tristimulus camera. Sorry, but the ONLY way you will
    get actual optical density values is to calibrate your system. Buy a grey scale
    wedge (any photo shop will have one, or go to Edmund Scientific) and use it to
    record an image in which the brightness of the various steps can be measured.
    Then construct a calibration curve of the density value for each step versus
    brightness. Whether you do that in Photoshop or ImageJ doesn't much matter, but
    note that you should NOT take the average brightness (on the 0..255) scale) of
    a region and convert that to density. Because the function is nonlinear, you
    need to convert the value of each pixel from 0..255 to density and then average
    the values. You should also expect the calibration to be pretty transient.
    Minor variations in line voltage will affect it, and so will warming up of the
    camera electronics. And if, God forbid, you have a camera with auto gain, then
    you can pretty much forget about getting anything useful. If you really want to
    get meaningful numbers you need to invest time in a) learning what is involved,
    and b) performing the calibration.
    DrJohnRuss, Aug 11, 2003
    #11
  12. "DrJohnRuss" <> wrote in message
    news:...
    SNIP
    > Bart is assuming that your recorded 0..255 values represent a linear

    measure
    > of the original transmitted light.


    Right, and that was probably assuming too much already... ;-) Thanks for
    stressing that.

    Bart
    Bart van der Wolf, Aug 12, 2003
    #12
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