How to scan microscopic cuts - Epson 4990

Discussion in 'Apple' started by Marc Heusser, Jun 29, 2006.

  1. Marc Heusser

    Marc Heusser Guest

    I try to scan microscopic cuts hoping to reach at least 100x
    magnification (9600 dpi scan -> 72 dpi screen).
    I tried it on a Mac using Epson Scan, set at 9600 dpi, using the
    transparency mode. I set the glass slides directly on the scanning glass
    (both upside down and upright).
    When I inspect the images, they seem to be much lower resolution (say
    4800 dpi).
    How do I best do that? Any experience?

    TIA

    Marc
     
    Marc Heusser, Jun 29, 2006
    #1
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  2. Marc Heusser

    CSM1 Guest

    No flatbed scanner has enough resolution to scan a microscope slide. Not to
    magnify 100X.

    You need a microscope with a digital camera attached.
     
    CSM1, Jun 29, 2006
    #2
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  3. Marc Heusser

    Marc Heusser Guest

    If you look at your film holders, you will see they don't place the image to
    be scanned directly on the glass. They suspend the film slightly off the
    glass. If you are scanning a mounted film slide, the slide mount keeps the
    film slightly of the glass. From your description, it sounds like your
    image is right on the glass as opposed to in a mount. You need to make sure
    your image is also slightly off the glass if you want the best resolution.[/QUOTE]

    Actually the microscope slides have a thick glass, and a thin one. I
    used both configurations, the thick one below gave the better scan. The
    actual tissue was therefore some 0.8 mm above the glass plate of the
    scanner. Maybe it needs more? I'll try to fix them int the film holders
    somehow. Would you know where the actual plane of focus lies?
    Epson claims a 4800x9600 optical resolution - it should be either 4800
    or 9600 that gives the best resolution. 2400 ppi definitely gives a
    worse scan. Epson claims an interpolated resolution of 12800 is possible.

    I'd certainly get a better picture this way - I do not have a
    photographic adapter though for my microscope (an 20y old Olympus CH2,
    goes up to 600x)

    But IF the scanner actuall gives the above mentioned 4800x9600
    resolution, when looking at the picture at 72 dpi screen resolution I
    should get a magnification of 67 to 134, ie roughly 100x. Unless the
    picture is not as sharp as given by the scanner's specs. And the scanner
    does scan in the transmissive mode.

    Thank you both

    Marc
     
    Marc Heusser, Jun 30, 2006
    #3
  4. Marc Heusser

    CSM1 Guest

    resolution.

    Actually the microscope slides have a thick glass, and a thin one. I
    used both configurations, the thick one below gave the better scan. The
    actual tissue was therefore some 0.8 mm above the glass plate of the
    scanner. Maybe it needs more? I'll try to fix them int the film holders
    somehow. Would you know where the actual plane of focus lies?
    Epson claims a 4800x9600 optical resolution - it should be either 4800
    or 9600 that gives the best resolution. 2400 ppi definitely gives a
    worse scan. Epson claims an interpolated resolution of 12800 is possible.

    I'd certainly get a better picture this way - I do not have a
    photographic adapter though for my microscope (an 20y old Olympus CH2,
    goes up to 600x)

    But IF the scanner actuall gives the above mentioned 4800x9600
    resolution, when looking at the picture at 72 dpi screen resolution I
    should get a magnification of 67 to 134, ie roughly 100x. Unless the
    picture is not as sharp as given by the scanner's specs. And the scanner
    does scan in the transmissive mode.

    Thank you both

    Marc
    [/QUOTE]


    This company has lens adapters for microscopes to various Digital Cameras.
    You have to choose the one for your camera and microscope.
    http://www.zarfenterprises.com/
     
    CSM1, Jun 30, 2006
    #4
  5. Actually the microscope slides have a thick glass, and a thin one. I
    used both configurations, the thick one below gave the better scan. The
    actual tissue was therefore some 0.8 mm above the glass plate of the
    scanner. Maybe it needs more? I'll try to fix them int the film holders
    somehow. Would you know where the actual plane of focus lies?
    Epson claims a 4800x9600 optical resolution - it should be either 4800
    or 9600 that gives the best resolution. 2400 ppi definitely gives a
    worse scan. Epson claims an interpolated resolution of 12800 is possible.

    I'd certainly get a better picture this way - I do not have a
    photographic adapter though for my microscope (an 20y old Olympus CH2,
    goes up to 600x)

    But IF the scanner actuall gives the above mentioned 4800x9600
    resolution, when looking at the picture at 72 dpi screen resolution I
    should get a magnification of 67 to 134, ie roughly 100x. Unless the
    picture is not as sharp as given by the scanner's specs. And the scanner
    does scan in the transmissive mode.

    Thank you both

    Marc
    [/QUOTE]
    Finding the focus is not difficult. You need a
    flat scale and something of know thickness to set
    it on. Best bet is a machinists scale, like the
    flat bar from a machinists square (or use an
    architects scale). Set one end on the glass and
    place a support of known thickness, e.g., a coin,
    at a specific distance and scan and check distance
    for best focus/ For example, 10mm high at 200mm
    length (or 1mm high per 20mm linear).
     
    George E. Cawthon, Jul 2, 2006
    #5
  6. Marc Heusser

    Marc Heusser Guest

    ....
    I will check - If I can I'd currently avoid the expense - but it
    certainly is the better option. Acutally I found a new review comparing
    the Epson V750 (newer, better successor of the 4990) compared to the
    Nikon 4000 - the dedicated film scanner IS better. And having a
    dedicated holder does make it easier. Thank you for the tip.

    Thank you - easy and very useful :)

    I guess I'll make do with my current scanner - at least up to when I'll
    get a dedicated Nikonn scanner for my slides. (I do have a few thousand
    photo slides too - although a commercial service might be useful there.)

    Marc
     
    Marc Heusser, Jul 2, 2006
    #6
  7. Marc Heusser

    Marc Heusser Guest

    I did it now - using a block of Post-It Notes as an easily adjustable
    fixed height block.
    My Epson 4990 seems to have maximum sharpness (ie focus) at between 1.2
    and 1.6 mm above the glass - the effect is quite noticeable at 9600 dpi.
    I'll scan at 4800 dpi.

    As a quick fix the Post-It Notes will also provide a suiteable ³holder³
    for now (scanning some 150 glass microscope slides for my own use).

    Thanks again

    Marc
     
    Marc Heusser, Jul 2, 2006
    #7
  8. Marc Heusser

    Marc Heusser Guest

    With the cut now in the plane of focus, test with both 4800 and 9600 dpi
    resolution are clear: 9600 is clearly superior in the Epson 4990,
    showing much more detail and less "grain" - so if you need this last bit
    of resolution it pays to use 9600 dpi. (It even shows when you compress
    with jpg afterwards.) Also this does not change when applying an unsharp
    mask filter.

    Marc
     
    Marc Heusser, Jul 2, 2006
    #8
  9. Marc Heusser

    NRen2k5 Guest

    Which for all intents and purposes is like scanning the image at 2400ppi
    and resampling ("resizing" in most graphics suites) to 4800ppi.
    That is *so* true. I don't feel any need to scan most material at any
    higher resolution than 600ppi, because even at that resolution, the
    individual ink dots in news and magazine graphics come through very clearly.

    I have even found that I can scan covers to audio-CD's and save them as
    8-bit PNG's... because at that high resolution (where you can
    dinstinguish individual ink dots), you no longer need anywhere near 17
    million colours.
     
    NRen2k5, Jul 2, 2006
    #9
  10. Marc Heusser

    NRen2k5 Guest

    Now onto the next order of business... getting your news client to use
    the proper encoding (or do you actually *mean* to use the exponent 3 as
    quotation marks? ;)
     
    NRen2k5, Jul 2, 2006
    #10
  11. Marc Heusser

    Marc Heusser Guest

    Just to clear that: the Epson 4990 has 4800x9600 dpi *optical*
    resolution - and scanning at 9600 gives much more detail.

    Nonetheless, this only applies if the original actually has that kind of
    resolution - this applies for my microscopic slides, (being real
    tissue), they have features down to less than 1um (eg nerves).
    But then we are using light of a wavelength eg 600 nanometres, so
    practical resolution is probably limited at 2 micrometres. (9600 dpi is
    2.6 micrometres). And the cuts are 6 micrometres or more thick.
    Very true for most materials - microscopic slides are exceptional in
    having details down to much less than 1 micrometre.

    Marc
     
    Marc Heusser, Jul 3, 2006
    #11
  12. Marc Heusser

    NRen2k5 Guest

    On the y-axis, anyway. On the x-axis, you're getting 4800dpi
    interpolated to 9600 when you scan at 9600.
    Yes and as already pointed out, scanning microscopic slides is not an
    intended use of a flatbed scanner. You will get better results with a
    microscope+camera combo.
     
    NRen2k5, Jul 3, 2006
    #12
  13. Perhaps you should take your own advice, the double quotation marks on
    Marc's original message showed as intended on my newsreader, not on
    your response.

    ;-)

    Bart
     
    Bart van der Wolf, Jul 3, 2006
    #13
  14. "Marc Heusser" <>
    wrote in message
    Yes, I've recommended something like that ever since the 2450 model,
    which shows an improved resolution in the "slow-scan" direction from
    half stepping the scan head. It thus samples twice as fine in that
    direction, and interpolates in the other direction to maintain aspect
    ratio. Since the interpolation doesn't add resolution but the double
    sampling does, one can choose to downsample by a factor of two
    afterwards and lose very lttle in one but gain resolution in the other
    direction.

    It pays to do that if the crop area is smallish, because other issues
    may be caused by the huge number of pixels of larger crops. How well
    it works depends on the original's detail, and the amount of actual
    overlap of the half stepped samples versus the scan lens resolution.

    Bart
     
    Bart van der Wolf, Jul 3, 2006
    #14
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