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Flatbed Scanners

Flatbed scanners are often overlooked when capturing digital images for a number of specimens in science and industry. With their high resolutions, even lighting, and expanded dynamic range, they are ideal for specimens often photographed with great difficulty on stereo microscopes. Scanners have the additional benefit of freedom from glare off reflective surfaces, which can contribute to a loss of visual data.

The better flatbed scanners are high in resolution and high in dynamic range. The resolution is reported incorrectly at two times the true, optical resolution, with the vertical resolution lower than the horizontal, because the vertical is controlled by a stepper motor (not as fine) and the horizontal by a row of microdetectors (much finer).

The dynamic range is determined by the lower (black) limit of the dynamic range using optical density units of measurement from 0.0 (white) to 4.0 (black). This limit is referred to as Density Maximum or Dmax. The best scanners have a Dmax of 4.0 and are preferred.

Flatbed scanners can be purchased with light sources in the top and bottom of the scanner so that transmissive (light going through the specimen) or reflective (light reflecting off the specimen) modes can be used.

Scanners often calibrate off the first 25 mm (~1 inch) of one end of the glass. Do not cover that area with the specimen or grayscale/color values will be dramatically altered. The calibration does not mean that a consumer flatbed scanner (versus a scanner intended for densitometry) can be used for imaging specimens destined for optical density measurements. Consumer scanners do not, as a rule, produce images with a gamma of 1: Such scanners may automatically apply a gamma of greater or less than 1, and the user has no control over the gamma settings. A calibration strip, such as a Stouffer step wedge, should be scanned and measured to determine whether or not gammas greater or less than 1 are applied before using the scanner for images from which optical densities will subsequently be measured.

Flatbed scanners meant for densitometric measurement, on the other hand, produce an image with a gamma of 1. These scanners do not include many of the settings described in the following section.

Prescan Settings for Flatbed Scanners

Before scanning a specimen or material, set the preferences in the scanning software according to the characteristics of your sample. Some possible settings are listed here (and shown in Figure 4.10 on next page):

  • Scan Mode: Normal. The scan mode contains presets for different kinds of materials. These presets can be chosen if desired to eliminate further choices except to prescan and scan. Note, however, that these settings may not provide adequate resolutions (Figure 4.10A).
  • Original. This setting concerns whether the original is transmissive (transparency) or reflective (Figure 4.10B).
  • Pos/Neg. The scanned material is positive unless the material is film; the film can be positive or negative. Even when the film is a negative (inverse image of a positive), it can be more desirable to scan the negative as a positive (retain the negative) and invert the image colors in Photoshop to produce a positive image (Figure 4.10C).
  • Scan Type. Choices are provided for binary (black or white, such as text or line art), grayscale, or color (Figure 4.10D).
  • Filter. None is the most desirable setting, because filters can be subsequently used in Photoshop with greater precision conforming to specific intents. The only exception might be the use of Descreening for eliminating or reducing dot patterns from published images and illustrations (Figure 4.10E).
  • Image Type. Generally, this option can be set to Standard. Color interpretation can be done in Photoshop (Figure 4.10F).
  • Scaling functions. These settings can be determined later when the output dimensions are known, so scaling would remain at 100%. If the output dimensions are known prior to scanning and they represent the only output for the image, set scaling before scanning (Figure 4.10G).
  • Microns per pixel. Settings may be available for microns per pixel on calibrated systems. When scanning features smaller than about 2 mm, less microns per pixel are desired (check with the manufacturer for specifics). Other specimens will likely contain enough pixel resolution at the greater microns/pixel settings (Figure 4.10H).
  • Bit Depth. Choose higher bit depth (Pixel Depth) even though it creates a larger file size (Figure 4.10I).
  • Output resolution. This is the resolution of the image that will be produced by the scanner in dots per inch (dpi). The net effect of this setting will be a resolution that matches pixels per inch (ppi) to dots per inch (dpi), though the two are not synonymous in practice (see note to the left). Laser printers and printing presses create dots, so this is a useful unit of measurement for those who print to pages for a living. To print at 1:1 to a printed page, 300 dpi is a large enough resolution setting. But when the specimen is small and will likely be enlarged to greater dimensions, 300 dpi will be inadequate. Because the final dimensions are often unknown or variable, depending on the output, this option can be set according to the size of the file or by the number of dots per inch (see next section). Set the output resolution after prescanning and outlining the area of interest (Figure 4.10J).
Figure 4.10

Figure 4.10 Several dialog boxes commonly found in software accompanying flatbed scanners.

General Procedure for Scanning

Once settings are determined for the specimen or material, the remaining steps involve prescanning—outlining the desired scan area and setting the output pixel resolution (Figure 4.11).

Figure 4.11

Figure 4.11 The image is prescanned (left), outlined (center), and Output resolution is then set (right).

  1. Click Prescan. The prescan image can be lower in resolution. It is only meant to provide enough resolution to make out the location of the specimen on the scanning bed. Colors and contrast may be way off as well: These will be corrected in later steps.
  2. Outline desired scan area. If the scanner is set to auto or if an auto setting is the default, colors and contrast may change at this point. The more closely the outline surrounds the specimen, the better the contrast and color settings. Alternatively, an Auto button can be clicked.
  3. Set Output resolution. Set the Output resolution of the specimen according to the file size when the final output is unknown. File size settings according to bit depth are suggested (Table 4.4) when desiring to preserve a target output resolution for publication. Maximum optical resolutions for the scanner are used when desiring the highest resolutions for small features, such as those found in 35 mm films or microscope slides. Note that text and line drawings for publication require 1200 dpi resolutions.

    Table 4.4. General Guidelines for File Size or DPI Setting









    Graphs, Line Drawings






    For easily resolved features by eye

    > 1 MB*

    1200 DPI

    >3 MB

    > 1.5 MB

    > 4.5 MB

    > 2 MB

    > 8 MB

    For Publication at 1:1 (dpi)








  4. Accept scanned image. If the contrast and color of the image are close to that of the specimen, click Scan to perform a final scan. When these do not appear correct, continue with remaining steps or correct by following post-processing steps in Photoshop.
  5. Levels/Curves buttons. If a consistent means is desired for scanning, both the Histogram (distribution of grayscale or color values) and the tonal Curve can be set manually (Figure 4.12). Return these functions to their original values to retain nonadjusted values or set them appropriately to the specimen. Record these values for scanning future specimens. More information on setting Levels and Curves can be found in Chapters 6 and 7.
Figure 4.12

Figure 4.12 Levels (top) and Curves (bottom) dialog boxes.

After slight adjustments to Levels (also shown in Curves), the final image is captured (Figure 4.13). Note the sharpness of the black end caps: They are not resting on the glass platen of the flatbed scanner; instead, they are raised 12 mm (0.5 inch) off the surface.

Figure 4.13

Figure 4.13 Final scan of a three-dimensional inking device.

Tips for Scanning

Additional information about films and documents is presented here for higher-quality results:

  • 35 mm slides, negatives, x-ray films, and microscope slides. Negatives and microscope slides require maximum optical resolution to retain visual information (Figure 4.14A). The inset in Figure 4.14A shows the level of detail from a specimen mounted on a microscope slide. Microscope slides and films may have to be lifted off the surface of the glass to prevent the formation of Newton's rings from moisture at the glass surface (Figure 4.14B). Films can be scanned at resolutions greater than 1500 dpi to retain resolution for most films. Lettering, line drawings, and symbols that are part of the slide image will never contain crisp edges and will have to be relettered and redrawn (Figure 4.14C). X-ray films can be lower in resolution and may not need to be scanned at resolutions higher than is required for print publication.
    Figure 4.14

    Figure 4.14 Examples of scanned specimens.

  • Pages from publications. Once copyright approval is given, printed pages from publications can be scanned. Images in print publications contain a dot pattern that can cross with the dot pattern of the computer screen to create a moiré pattern (and look somewhat like Newton's rings in Figure 4.14B), which is visible except when the image is zoomed in. The dot pattern can be ameliorated by descreening via scanner software or eliminated in postprocessing by removing periodic noise in Fourier space (which is outside the scope of this book). Pages from books are scanned with black paper behind pages so that inks from the reverse side are not detected.
  • Eliminating colored lines or grids. Colored lines that are part of a printed page can be removed after scanning in color. If the lines contain red, green, or blue, channels can be split in Photoshop to find a grayscale image sans the lines (see "Grayscale Channel with Highest Contrast" in Chapter 9, "Separating Relevant Features from the Background").
  • Line drawings, graphs, and poorly printed text. Scan these items as grayscale or color, and be sure that the background is not pure white. Often lines become faint along their lengths: To retain that information, gray values are necessary. Increase contrast and brightness in Photoshop using Levels or Curves (see "Graphic Images" in the "Problem Images" section of Chapter 6). If, however, text is being scanned for text recognition (Optical Character Recognition [OCR]), these pages are scanned as black and white with no shades of gray.
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