GRUPO 1 : digital manipulation of bright field and florescence images noise reduction contrast enhancement and feature extraction


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GRUPO 1 : digital manipulation of bright field and florescence images noise reduction contrast enhancement and feature extraction

  1. 1. CHAPTER 14 Digital Manipulation of Brightfield and Fluorescence Images: Noise Reduction, Contrast Enhancement, and Feature Extraction Richard A. Cardullo* and Edward H. HinchcliVe† *Department of Biology, The University of California Riverside, California 92521 † Department of Biological Sciences University of Notre Dame, Notre Dame, Indiana 46556 I. Introduction II. Digitization of Images III. Using Gray Values to Quantify Intensity in the Microscope IV.Noise Reduction A. Temporal Averaging B. Spatial Methods V. Contrast Enhancement VI. Transforms, Convolutions, and Further Uses for Digital Masks A. Transforms B. Convolution C. Digital Masks as Convolution Filters VII. Conclusions References I. Introduction The theoretical basis of image processing along with its applications is an extensive topic that cannot be adequately covered here but has been presented in a number of texts dedicated exclusively to this topic (Andrews and Hunt, 1977;METHODS IN CELL BIOLOGY, VOL. 81 0091-679X/07 $35.00Copyright 2007, Elsevier Inc. All rights reserved. 285 DOI: 10.1016/S0091-679X(06)81014-9
  2. 2. 286 Richard A. Cardullo and Edward H. HinchcliVe Bates and McDonnell, 1986; Chellappa and Sawchuck, 1985; Gonzalez and Wintz, 1987; Inoue and Spring, 1997; Russ, 1994; Shotton, 1993). In this chapter, the basic principles of image processing used routinely by microscopists will be presented. Since image processing allows the investigator to convert the microscope/detector system into a quantitative device, this chapter will focus on three basic problems: (1) reducing ‘‘noise,’’ (2) enhancing contrast, and (3) quantifying intensity of an image. These techniques can then be applied to a number of diVerent methodolo- gies such as video-enhanced diVerential interference microscopy (VEDIC; Chapter 16 by Salmon and Tran, this volume), nanovid microscopy, fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, fluorescence reso- nance energy transfer, and fluorescence ratio imaging (Cardullo, 1999). In all cases, knowledge of the basic principles of microscopy, image formation, and image-processing routines is absolutely required to convert the microscope into a device capable of pushing the limits of resolution and contrast. II. Digitization of Images An image must first be digitized before an arithmetic, or logical, operation can be performed on it (Pratt, 1978). For this discussion, a digital image is a discrete representation of light intensity in space (Fig. 1). A particular scene can be viewed as being continuous in both space and light intensity and the process of digitization converts these to discrete values. The discrete representation of intensity is com- monly referred to as gray values whereas the discrete representation of position is given as picture elements, or pixels. Therefore, each pixel has a corresponding gray value which is related to light intensity [e.g., at each coordinate (x,y) there is a corresponding gray value designated as GV(x,y)]. The key to digitizing an image is to provide enough pixels and grayscale values to adequately describe the original image. Clearly, the fidelity of reproduction between the true image and the digitized image depends on both the spacing between the pixels (e.g., the number of bits that map the image) and the number of gray values used to describe the intensity of that image. Figure 1B shows a theoretical one-dimensional scan across a portion of an image. Note that the more pixels used to describe, or sample, an image, the better the digitized image reflects the true nature of the original. Conversely, as the number of pixels is progressively reduced, the true nature of the original image is lost. When choosing the digitizing device for a microscope, particular attention must be paid to matching the resolution limit of the microscope ($0.2 mm for visible light, see Chapter 1 by Sluder and Nordberg, this volume) to the resolution limit of the digitizer (Inoue, 1986). A digitizing array that has an eVective separa- tion of 0.05 mm per pixel is, at best, using four pixels to describe resolvable objects in a microscope resulting in a highly digitized representation of the original image (note that this is most clearly seen when using the digitized zoom feature of many imaging devices which results in a ‘‘boxy’’ image representation). In contrast, a
  3. 3. 14. Digital Manipulation of Brightfield and Fluorescence Images 287 A B 60 60 50 50 Gray value Intensity 40 40 30 30 20 20 0 2 4 6 8 10 0 5 10 15 20 25 30 Position (mm) Pixel number C D 60 60 50 50 Gray value Gray value 40 40 30 30 20 20 0 4 8 12 16 0 2 4 6 8 Pixel number Pixel number Fig. 1 (A) A densitometric line scan through a microscopic image is described by intensity values on the y-axis and its position along the x-axis. (B) A 6-bit-digitized representation (64 gray values) of the object in (A), with 32 bits used to describe the position across 10 mm. The digital representation captures the major details of the original object but some finer detail is lost. Note that the image is degraded further when the position is described by only (C) 16 bits or (D) 8 bits. digitizer which has pixel elements separated by 1 mm eVectively averages gray values five times above the resolution limit of the microscope resulting in a degraded representation of the original image. In addition to assigning the number of pixels for an image, it is also important to know the number of gray values needed to faithfully represent the intensity of that image. In Fig. 1B, the original image has been digitized at 6-bit resolution (6 bits ¼ 26 ¼ 64 gray values from 0 to 63). The image could be better described by more gray values (e.g., 8 bits ¼ 256 gray levels) but would be poorly described by less gray values (e.g., 2 bits ¼ 4 gray values). The decision on how many pixels and gray values are needed to describe an image is dictated by the properties of the original image. Figure 1 represents a low- contrast, high-resolution image which needs many gray scales and pixels to adequately describe it. However, some images are by their very nature high
  4. 4. 288 Richard A. Cardullo and Edward H. HinchcliVe contrast and low resolution and require less pixels and gray values to describe it (e.g., a line drawing may require only 1 bit of gray-level depth, black or white). Ultimately, the trade-oV is one in contrast, resolution, and speed of processing. The more descriptors used to represent an image, the slower the processing routines will be performed. In general, an image should be described by as few pixels and gray values as needed so that speed of processing can be optimized. For many applications, the user can select a narrower window, or region of interest (ROI), within the image to speed up processing. III. Using Gray Values to Quantify Intensity in the Microscope A useful feature shared by all image processors is that they allow the microsco- pist a way to quantify image intensity values into some meaningful parameter (Green, 1989; Russ, 1990). In standard light microscopy, the light intensity—and therefore the digitized gray values—is related to the optical density (OD) which is proportional to the log of the relative light intensity. In dilute solutions (i.e., in the absence of significant light scattering), the OD is proportional to the concentra- tion of absorbers, C, the molar absorptivity, e, and the path length, l, through the vessel containing the absorbers. In such a situation, the OD is related to these parameters using Beer’s law: I0 OD ¼ log ¼ eCl I where I and I0 are the intensities of light in the presence and absence of absorber, respectively. Within dilute solutions, it therefore might be possible to equate a change in OD with changes either in molar absorptivity, path length, or concen- tration. However, with objects as complex as cells, all three parameters can vary tremendously and the utility of using OD to measure a change in any one parameter is diYcult. Although diYcult to interpret in cells, measuring changes in digitized gray values in an OD wedge oVers the investigator a good way to calibrate an entire microscope system coupled to an image processor. Figure 2 shows such a calibra- tion using a brightfield microscope coupled to a CCD camera and an image processor. The wedge had 0.15-OD increments. The camera/image processor unit was digitized to 8 bits (0–255) and the median gray value was recorded for a 100 Â 100 pixel array (the ROI) in each step of the wedge. In this calibration, the black level of the camera was adjusted so that the highest OD corresponded to a gray value of 5. At the other end of the scale (the lowest OD used), the relative intensity was normalized so that I/I0 was equal to 1 and the corresponding gray value was $95% of the maximum gray value ($243). As seen in Fig. 2, as the step wedge is moved through the microscope, the median value of the gray value increased as the log of I/I0. In addition to acting as a useful calibration, this figure
  5. 5. 14. Digital Manipulation of Brightfield and Fluorescence Images 289 200 100 70 Gray value 50 30 20 10 5 0.03 0.1 0.3 1 Relative intensity Fig. 2 Calibration of a detector using an image processor. The light intensity varied incrementally using an OD step wedge (0.15-OD increments), and the gray value was plotted as a function of the normalized intensity. In this instance the camera/image processor system was able to quantify diVer- ences in light intensity over a 40-fold range. shows that an 8-bit processor can reliable quantify changes in light intensity over two orders of magnitude. IV. Noise Reduction The previous sections have assumed that the object being imaged is relatively free of noise and is of suYcient contrast to generate a usable image. Although this may be true in some instances, the ultimate challenge in many applications is to obtain reliable quantitative information from objects which produce a low-contrast, noisy signal (Erasmus, 1982). This is particularly true in cell physiological measurements using specialized modes of microscopy such as VEDIC, fluorescence ratio imaging, nanovid microscopy, and so on. There are diVerent ways to reduce noise and the methods of noise reduction chosen depend on many diVerent factors, including the source of the noise, the type of camera employed for a particular application, and the contrast of the specimen. For the purposes of this chapter, we shall distinguish between temporal and spatial techniques to increase the signal-to-noise ratio (SNR) of an image.A. Temporal Averaging In most low-light level applications, there is considerable amount of shot noise associated with the signal. If quantitation is needed, it is often necessary to reduce the amount of shot noise in order to improve the SNR. Because this type of noise reduction requires averaging over a number of frames (!2 frames), this method is
  6. 6. 290 Richard A. Cardullo and Edward H. HinchcliVe best used for static objects. Clearly, temporal averaging can be diYcult to use for optimizing contrast for dynamic processes such as cell movement, detecting rapid changes in intracellular ion concentrations over time, quantifying molecular mo- tions using fluorescence recovery after photobleaching, or single particle tracking. The trade-oV is between improving SNR versus blurring or missing the capture of a dynamic event. Current digital microscopy equipment allows for very short exposure times, even with the low-light levels associated with live cell imaging. Thus, frame averaging can be an acceptable solution to improve SNR, provided that the light exposures are suYciently short (Fig. 3). Assume that at any given time, t, within a given pixel, a signal, Si(t), represents both the true image, I, which may be inclusive of background, and some source of noise, Ni(t). Since the noise is stochastic in nature, Ni(t) will vary in time, taking on both positive and negative values, and the signal, Si(t), will vary about some mean value. For each frame, the signal is therefore just: Si ðtÞ ¼ I þ Ni ðtÞ As the signal is averaged over M frames, an average value for Si(t) and Ni(t) is obtained: hSi iM ¼ I þ hNi iM where hSiiM and hNiiM represent the average value of Si(t) and Ni(t) over M frames. As the number of frames, M, goes to infinity, the average value of Ni goes to zero and therefore: hSi iM!1 ¼ I The question facing the microscopist is how large M should be so the SNR is acceptable. This is determined by a number of factors including the magnitude of the original signal, the amount of noise, and the degree of precision required by the particular quantitative measurement. A quantitative measure of noise reduc- tion can be obtained by looking at the standard deviation of the noise, which decreases inversely as the square root of the number of frames (sM ¼ s0/√M). Therefore, averaging a field for 4 frames will give a 2-fold improvement in the SNR, averaging for 16 frames yields a 4-fold improvement, while averaging for 256 frames yields a 16-fold improvement. At some point the user obviously reaches a point of diminishing returns where the noise level is below the resolution limit of the digitizer and any improvement in SNR is minimal (Fig. 4). Although frame-averaging techniques are not always appropriate for moving objects, it is possible to apply a running average where the resulting image is a weighted sum of all previous frames. Because the image is constantly updated on a frame-by-frame basis, these types of recursive techniques are useful for following moving objects but improvement in SNR is always less than that obtained with the simple averaging technique outlined in the previous paragraph (Erasmus, 1982).
  7. 7. No frame averaging 4ϫ frame averaging 8ϫ frame averagingFig. 3 Frame averaging improves the SNR. A dividing mammalian cell expressing GFP-a tubulin was imaged using a spinning diskconfocal microscope. Images were collected with no frame averaging, 4 frames averaged or 8 frames averaged. Random noise is reduced dueto frame averaging.
  8. 8. 292 Richard A. Cardullo and Edward H. HinchcliVe 1.0 1.0 0.8 0.8 0.6 0.4 0.6 0.2 Noise 0.0 0 2 4 6 8 10 12 14 16 0.4 0.2 0.0 0 32 64 96 128 160 192 224 256 Number of frames averaged Fig. 4 Reduction in noise as a function of the numbers of frames averaged. The noise is reduced inversely as the square root of the number of frames averaged. In this instance, the noise was normalized to the average value obtained for a single frame. The major gain in noise reduction is obtained after averaging very few frames (inset) and averaging for more than 64 frames leads to only minor gains in the SNR. Additional recursive filters are possible which optimize the SNR but these are typically not available on commercial image processors.B. Spatial Methods A number of spatial techniques are available which allow the user to reduce noise on a pixel-by-pixel basis. The simplest of these techniques generally uses simple arithmetic operations within a single frame or, alternatively, between two diVerent frames. In general, these types of routines involve either image subtrac- tion or division from a background image or calculate a mean or median value around the neighborhood of a particular pixel. More sophisticated methods use groups of pixels (known as masks, kernels, or filters), which perform higher-order functions to extract particular features from an image. These types of techniques will be discussed separately in Section VI.
  9. 9. 14. Digital Manipulation of Brightfield and Fluorescence Images 2931. Arithmetic Operations Between an Object and a Background Image If one has an image, which has a constant noise component in a given pixel in each frame, the noise component can be removed by performing a simple subtrac- tion that removes the noise and optimizes the SNR. Although SNR is improved, subtraction methods can also significantly decrease the dynamic range but these problems can generally be avoided when the microscope and camera systems are adjusted to give the optimal signal. Any constant noise component can be removed by subtraction and, in general, it is always best to subtract the noise component from a uniform background image (Fig. 5). Thus, if a pixel within an image has a gray value of say 242, with the background having a gray value of 22 in that same pixel, then a simple A B 250 250 200 200 Gray value Gray value 150 150 100 100 50 50 0 0 0 10 20 30 40 50 60 0 10 20 30 40 50 60 Pixel number Pixel number C 250 200 Gray value 150 100 50 0 0 10 20 30 40 50 60 Pixel number Fig. 5 Subtracting noise from an image. (A) Line scan across an object and the surrounding background. (B) Line scan across the background alone reveals variations in intensity that may be due to uneven light intensity across the field, camera defects, dirt on the optics, and so on. (C) Image in (A) subtracted from image in (B). The result is a ‘‘cleaner’’ image with a higher SNR in the processed image compared to the original in (A).
  10. 10. 294 Richard A. Cardullo and Edward H. HinchcliVe subtraction would yield a resultant value of 220. Image subtraction therefore preserves the majority of the signal, and the subtracted image can then be pro- cessed further using other routines. In order to reduce temporal noise, both images can be first averaged as described in Section IV.A.2. Concept of a Digital Mask A number of mathematical manipulations of images involve using an array (or a digital mask) around a neighborhood of a particular pixel. These digital masks can be used either to select particular pixels from the neighborhood (as in averaging or median filtering discussed in Section IV.B.3) or alternatively can be used to apply some mathematical weighting function to an image on a pixel-by-pixel basis to extract particular features from that image (discussed in detail in Section VI). When the mask is overlaid on an image, the particular mathematical operation is per- formed and the resultant value is placed into the same array position and the operation is performed repeatedly until the entire image has been transformed. Although a digital mask can take on any shape, the most common masks are square with the center pixel being the particular pixel being operated on at any given time (Fig. 6). The most common masks are 3 Â 3 or 5 Â 5 arrays so that only the nearest neighbors will have an eVect on the pixel being operated on. Additionally, larger arrays will greatly increase the number of computations that need to be performed which can significantly slow down the rate of processing a particular image. px − 1,y + 1 px,y + 1 px + 1,y + 1 px − 1,y px,y px + 1,y px − 1,y − 1 px,y − 1 px + 1,y − 1 Fig. 6 Digital mask used for computing means, averages, and higher-order mathematical operations, especially convolutions. In the case of the median and average filters, the mask is overlaid over each pixel in the image and the resultant value is calculated and placed into the identical pixel location in a new image buVer.
  11. 11. 14. Digital Manipulation of Brightfield and Fluorescence Images 2953. Averaging Versus Median Filters When an image contains random and infrequent intensity spikes with particular pixels, a digital mask can be used around each pixel to remove them. Two common ways to remove these intensity spikes are to calculate either the average value or the median value within the neighborhood and assign that value to the center pixel in the processed image (Fig. 7). The choice of filter used will depend on the type of processed image that is desired. Although both types of filters will A 200 23 25 26 192 27 47 52 56 55 59 150 Gray value 26 27 23 27 135 42 55 116 52 61 117 26 28 29 31 175 52 56 57 59 25 28 19 31 186 49 5 57 56 52 100 29 27 178 57 30 51 195 7 55 57 26 22 26 42 12 46 57 55 142 54 50 0 2 4 6 8 Position 100 80 Gray value B 36 45 58 78 68 72 61 63 60 35 26 57 78 81 67 56 63 40 53 47 65 71 86 72 60 51 20 42 48 65 56 71 58 70 59 0 2 4 6 8 Position 100 C 80 Gray value 26 27 28 42 52 55 55 57 27 27 29 42 52 56 56 57 60 28 28 31 49 51 52 56 56 40 26 28 31 46 49 51 56 55 20 0 2 4 6 8 Position Fig. 7 Comparison of 3 Â 3 averaging and median filters to reduce noise. (A) Digital representation of an image displaying gray values at diVerent pixel locations. In general, the object possesses a boundary which is detected as a line scan from left to right. However, the image has a number of intensity spikes which significantly mask the true boundary. A line scan across a particular row (row denoted by arrow and scan is on the right-hand side) reveals both high- and low-intensity values which greatly distort the image. (B) When a 3 Â 3 averaging filter is applied to the image, the extreme intensity values are significantly reduced but the image is smoothed in the vicinity of the boundary. (C) In contrast, a 3 Â 3 median filter removes the extreme intensity values while preserving the true nature of the boundary.
  12. 12. 296 Richard A. Cardullo and Edward H. HinchcliVe degrade an image, the median filter preserves edges better than the averaging filter since all values with the digital mask are used to compute the mean. Further, averaging filters are seldom used to remove intensity spikes because the spikes themselves contribute to the new intensity value in the processed image and therefore the resultant image is blurred. The median filter is more desirable for removing infrequent intensity spikes from an image since those intensity values are always removed from the processed image once the median is computed. In this case, any spike is replaced with the median value within the digital mask, which gives a more uniform appearance to the processed image. Hence, a uniform background that contains infrequent intensity spikes will look absolutely uniform in the processed image. Since the median filter preserves edges (a sharpening filter), it is often used for high-contrast images (Fig. 8). Fig. 8 EVects of median sharpen and smooth filters on image contrast. A dividing mammalian cell expressing GFP-a tubulin was imaged using a spinning disk confocal microscope. After collection, separate digital filters were applied to the image.
  13. 13. 14. Digital Manipulation of Brightfield and Fluorescence Images 297 V. Contrast Enhancement One of the most common uses of image processing is to digitally enhance the contrast of the image using a number of diVerent methods (Castleman, 1979). In brightfield modes such as phase contrast or diVerential interference contrast, the addition of a camera and an image processor can significantly enhance the contrast so that specimens with inherent low contrast can be observed. Addition- ally, contrast routines can be used to enhance an image in a particular region, which may allow the investigator to quantify structures or events not possible with the microscope alone. This is the basis for VEDIC, which allows, for example, the motion of low-contrast specimens such as microtubules or chromosomes to be quantified (Chapter 16 by Salmon and Tran, this volume). In order to optimize contrast enhancement digitally, it is imperative that the microscope optics and the camera be adjusted so that the full dynamic range of the system is utilized. This is discussed further in Chapter 17 by Wolf et al., this volume. The gray values of the image and background can then be displayed as a histogram (Fig. 9) and the user is then able to adjust the brightness and contrast within a particular region of the image. Within a particular gray value range, the user can then stretch the histogram so that values within that range are spread out over a diVerent range in the processed image. Although this type of contrast enhancement is artificial, this allows the user to discriminate features which otherwise may not have been detectable by eye in the original image. Stretching gray values over a particular range in an image is one type of mathematical manipulation, which can be performed on a pixel-by-pixel basis. In general, any digital image can be mathematically manipulated to produce an image with diVerent gray values. The user-defined function that transforms the original function is known as the image transfer function (ITF), which specifies the value and the mathematical operation that will be performed on the original image. This type of operation is a point operation, which means that the output gray value of the ITF is dependent only on the input gray value on a pixel-by-pixel basis. The gray values of the processed image, I2, are therefore transformed at every pixel location relative to the original image using the same ITF. Hence, every gray value in the processed image is transformed according the generalized relationship: GV2 ¼ f ðGV1 Þ where GV2 is the gray value at every pixel location in the processed image, GV1 is the input gray value of the original image, and f(GV1) is the ITF acting on the original image. The simplest type of ITF is a linear equation of slope m and intercept b: GV2 ¼ mGV1 þ b
  14. 14. 298 Richard A. Cardullo and Edward H. HinchcliVe A B 3000 3000 2500 2500 Number of pixels Number of pixels 2000 2000 1500 1500 1000 1000 500 500 0 0 0 50 100 150 200 250 0 50 100 150 200 250 Gray value Gray value C 3000 2500 Number of pixels 2000 1500 1000 500 0 0 50 100 150 200 250 Gray value Fig. 9 Histogram representation of gray values for an entire image. (A) The image contains two distributions of intensity over the entire gray value range (0–255). (B) The lower distribution can be removed either through subtraction (if lower values are due to a uniform background) or by applying the appropriate ITF which assigns a value of 0 to all input pixels having a gray value less than 100. The resulting distribution contains only information from input pixels with a value greater than 100. (C) The histogram of the higher distribution can be stretched to fill the lower gray values resulting in a lower mean value than the original. In this case, the digital contrast of the processed image is linearly transformed with the brightness and contrast determined by both the value of the slope and intercept chosen. In the most trivial case, choosing values of m ¼ 1 and b ¼ 0 would leave all gray values of the processed image identical to the original image (Fig. 10A). Raising the value of the intercept while leaving the slope unchanged would have the eVect of increasing all gray values by some fixed value (identical to increasing the DC or black level control on a camera). Similarly, decreasing the value of the intercept will produce a darker image than the original. The value of the slope is known as the contrast enhancement factor and changes in the value of m will have significant eVects on how the gray values are distributed in an image. A value of m 1 will have the eVect of spreading out the gray values over a wider range in the processed image relative to the original image. Conversely, values of m 1 will reduce the number of gray values used to describe a processed image
  15. 15. 14. Digital Manipulation of Brightfield and Fluorescence Images 299 A 250 250 200 200 Gray value 150 150 GV2 100 100 50 0 50 0 B 250 250 200 200 Gray value 150 150 GV2 100 100 50 50 0 0 C 250 250 200 200 Gray value 150 150 GV2 100 100 50 50 0 0 0 10 20 30 40 50 60 0 50 100 150 200 250 Pixel number GV1 Fig. 10 Application of diVerent linear ITFs to a low-intensity, low-contrast image. (A) Intensity line scan through an object which is described by few gray values. Applying a linear ITF with m ¼ 1 and b ¼ 0 (right) will result in no change from the initial image. (B) Applying a linear ITF with m ¼ 5 and b ¼ 0 (right) leads to significant improvement in contrast. (C) Applying a linear ITF with m ¼ 2 and b ¼ 50 (right) slightly improves contrast and increases the brightness of the entire image. relative to the original (Fig. 10). As noted by Inoue (1986), although linear ITFs can be useful, the same eVects can be best achieved by properly adjusting the camera’s black levels and gain controls. However, this may not always be practical if conditions under the microscope are constantly changing or if this type of contrast enhancement is needed after the original images are stored.
  16. 16. 300 Richard A. Cardullo and Edward H. HinchcliVe The ITF is obviously not restricted to linear functions, and nonlinear ITFs can be extremely useful for enhancing particular features of an image while eliminating or reducing others (Fig. 11). Nonlinear ITFs are also useful for correcting sources of nonlinear response in an optical system or to calibrate the light response of an A 250 250 200 200 Gray value 150 150 GV2 100 100 50 0 50 0 B 250 180 160 200 140 Gray value 120 150 GV2 100 100 80 60 50 40 20 0 C 250 250 200 200 Gray value 150 150 GV2 100 100 50 50 0 0 0 10 20 30 40 50 60 0 50 100 150 200 250 Pixel number GV1 Fig. 11 Application of diVerent nonlinear ITFs to the same low-intensity, low-contrast image in Fig. 8. (A) Initial image and ITF (right) resulting in no change. (B) Application of a hyperbolic ITF (right) to the image results in amplification of lower input values and only slightly increases the gray values for higher input values. (C) Application of a Gaussian ITF (right) to the image results in amplification of low values, with an oVset, and minimizes input values beyond 100.
  17. 17. 14. Digital Manipulation of Brightfield and Fluorescence Images 301 optical system (Inoue, 1986). The actual form of the ITF, being linear or nonlinear, is generally application dependent and user defined. For example, nonlinear ITFs that are sigmoidal in shape are useful for enhancing images, which compress the contrast in the center of the histogram and increase contrast in the tail regions of the histogram. This type of enhancement would be useful for images where most of the information about the image is in the tails of the histogram while the central portion of the histogram contains mostly background information. One type of nonlinear ITF, which is sigmoidal in shape, will enhance an 8-bit image of this type is given by the equation: 128 GV2 ¼ ½ðb À cÞa À ðb À GV1 Þa þ ðGV1 þ cÞa Š ðb À cÞa where b and c are the maximum and minimum gray values for the input image, respectively and are arbitrary contrast enhancement factors (Inoue, 1986). For values of a ¼ 1, this normally sigmoidal ITF becomes linear with a lope of 256(b À c). As a increases beyond 1, the ITF becomes more sigmoidal in nature with greater compression occurring at the middle gray values. In practice, ITFs are generally calculated in memory using a lookup table (LUT). An LUT represents the transformation that is performed on each pixel on the basis of that intensity value (Figs. 12 and 13). In addition to LUTs, which 1.0 A 0.8 Input light intensity 0.6 B 0.4 0.2 C D 0.0 0 50 100 150 200 250 Output gray value Fig. 12 Some diVerent gray value LUTs used to alter contrast in images. (A) Inverse LUT, (B) logarithmic LUT, (C) square root LUT, (D) square LUT, and (E) exponential LUT. Pseudo- color LUTs would assign diVerent colors instead of gray values.
  18. 18. 302 Richard A. Cardullo and Edward H. HinchcliVe A B C D Fig. 13 DiVerent LUTs applied to the image of a check cell. (A) No filter, (B) reverse contrast LUT, (C) square root LUT, (D) pseudo-color LUT.
  19. 19. 14. Digital Manipulation of Brightfield and Fluorescence Images 303 perform particular ITFs, LUTs are also useful for pseudo-coloring images where particular user-defined colors represent gray values in particular ranges. This is particularly useful in techniques such as ration imaging where color LUTs are used to represent concentrations of Ca2þ, pH, or other ions, when various indicator dyes are employed within cells. VI. Transforms, Convolutions, and Further Uses for Digital Masks In the previous sections, the most frequently used methods for enhancing contrast and reducing noise using temporal methods, simple arithmetic opera- tions, and LUTs were described. However, more advanced methods are often needed to extract particular features from an image which may not be possible using these simple methods (Jahne, 1991). In this section, some of the concepts and applications associated with transforms and convolutions will be introduced.A. Transforms Transforms take an image from one space to another. Probably, the most used transform is the Fourier transform which takes one from coordinate space to spatial frequency space (see Chapter 2 by Wolf, this volume for a discussion of Fourier transforms). In general, a transform of a function in one dimension has the form: X TðuÞ ¼ f ðxÞgðx; uÞ x where T(u) is the transform of f(x) and g(x,u) is known as the forward transformation kernel. Similarly, the inverse transform is given by the relation: X f ðxÞ ¼ TðuÞhðx; uÞ u where h(x,u) is the inverse transformation kernel. In two dimensions, these transformation pairs simply become: XX Tðu; vÞ ¼ f ðx; yÞgðx; y; u; vÞ x y XX f ðx; yÞ ¼ Tðu; vÞhðx; y; u; vÞ u v It is the kernel functions that provide the link, which brings a function from one space to another. The discrete forms shown above suggest that these operations can be performed on a pixel-by-pixel basis and many transforms in image processing
  20. 20. 304 Richard A. Cardullo and Edward H. HinchcliVe are computed in this manner (known as a discrete Fourier transform or DFT). However, DFTs are generally approximated using diVerent algorithms to yield a fast Fourier transform, or FFT. In the Fourier transform, the forward transformation kernel is: 1 À2piux gðx; uÞ ¼ e N and the reverse transformation kernel is: 1 þ2piux f ðx; uÞ ¼ e N Hence, a Fourier transform is achieved by multiplying a digitized image pixel-by- pixel whose gray value is given by f(x,y) by the forward transformation kernel given above. Transforms, and in particular Fourier transforms, can make certain mathematical manipulations of images considerably easier than if they were performed in coordinate space directly. One example where conversion to frequency space using an FFT is useful is in identifying both high- and low-frequency components on an image that allows one to make quantitative choices about information that can be either used or dis- carded. Sharp edges and many types of noise will contribute to the high-frequency content of an image’s Fourier transform. Image smoothing and noise removal can therefore be achieved by attenuating a range of high-frequency components in the transform range. In this case, a filter function, F(u,v), is selected that eliminates the high-frequency components of that transformed image, I(u,v). The ideal filter would simply cut oV all frequencies about some threshold value, I0 (known as the cutoV frequency): F ðu; vÞ ¼ 1 if jIðu; vÞj I0 F ðu; vÞ ¼ 0 if jIðu; vÞj I0 The absolute value brackets refer to the fact that these are zero-phase shift filters because they do not change the phase of the transform. A graphical representation of an ideal low-pass filter is shown in Fig. 14. Just as an image can be blurred by attenuating high-frequency components using a low-pass filter, so they can be sharpened by attenuating low-frequency components (Fig. 14). In analogy to the low-pass filter, an ideal high-pass filter has the following characteristics: F ðu; vÞ ¼ 0 if jIðu; vÞj I0 F ðu; vÞ ¼ 1 if jIðu; vÞj I0 Although useful, Fourier transforms can be computationally intense and are still not routinely used in most microscopic applications of image processing. A mathematically related technique known as convolution, which utilizes digital
  21. 21. 14. Digital Manipulation of Brightfield and Fluorescence Images 305 Low pass High pass A B F (u,v ) F (u,v ) 1 1 0 I (u,v ) 0 I(u,v ) I0 I0 Fig. 14 Frequency domain cutoV filters. The filter function in frequency space, F(u,v), is used to cut oV all frequencies above or below some cutoV frequency, I0. (A) A high-pass filter attenuates all frequencies below I0 leading to a sharpening of the image. (B) A low-pass filter attenuates all frequencies above I0 which eliminates high-frequency noise but leads to smoothing or blurring of the image. masks to select particular features of an image, is the preferred method of microscopists since many of these operations can be performed at faster rates and perform the mathematical operation in coordinate space instead of frequency space. These operations are outlined in Section VI.B.B. Convolution The convolution of two functions, f(x) and g(x), is given mathematically by: Z þ1 f ðaÞgðx À aÞda À1 where a is a dummy variable of integration. It is easiest to visualize the mechanics of convolution graphically as demonstrated in Fig. 15, which, for simplicity, shows the convolution for two square pulses. The convolution can be broken down into three simple steps: 1. Before carrying out the integration, reflect g(a) about the origin, yielding g(Àa) and then displace it by some distance x to give g(x À a). 2. For all values of x, multiply f(a) by g(x À a). The product will be nonzero at all points where the functions overlap. 3. Integrating this product yields the convolution between f(x) and g(x). Hence, the properties of the convolution are determined by the independent function f(x) and a function g(x) that selects for certain desired details in the function f(x). The selecting function g(x) is therefore analogous to the forward transformation kernel in frequency space except that it selects for features in coordinate space instead of frequency space. This clearly makes the convolution an important image-processing technique for microscopists who are interested in feature extraction.
  22. 22. 306 Richard A. Cardullo and Edward H. HinchcliVe A f (x) B g(x) 2 ϫ 1 x x 0 1 0 1 C f (x) g(x) 2 x 0 2 Fig. 15 Graphical representation of one-dimensional convolution. (A) In this simple example, the function, f(x), to be convolved is a square pulse of equal height and width. (B) The convolving function, g(x), is a rectangular pulse which is twice as high as it is wide. The convolving function is then reflected and is then moved from À1 to þ1. (C) In all areas where there is no overlap, the products of f(x) and g(x) is zero. However, g(x) overlaps f(x) in diVerent amounts from x ¼ 0 to x ¼ 2 with maximum overlap occurring at x ¼ 1. The operation therefore detects the trailing edge of f(x) at x ¼ 0 and the convolution results in a triangle which increases in height from 0 to 2 for 0 x 1 and decreases in height from 2 to 0 for 1 x 2. One simple application of convolutions is the convolution of a function with an impulse function (commonly known as a delta function), d(x À x0): Z þ1 f ðxÞdðx À x0 Þdx ¼ f ðx0 Þ À1 For our purposes, d(x À x0) is located at x ¼ x0 and the intensity of the impulse is determined by the value f(x) at x ¼ x0 and is zero everywhere else. In this example, we will let the kernel g(x) represent three impulse functions separated by a period, t: gðxÞ ¼ dðx þ tÞ þ dðxÞ þ dðx À tÞ As shown in Fig. 16, the convolution of the square pulse f(x) with these three impulses results in a copying of f(x) at the impulse points.
  23. 23. 14. Digital Manipulation of Brightfield and Fluorescence Images 307 A f(x) B g(x ) ϫ x x −t 0 +t C f (x) g (x) x −t 0 +t Fig. 16 Using a convolution to copy an object. (A) The function f(x) is a rectangular pulse of amplitude, A, with its leading edge at x ¼ 0. (B) The convolving functions g(x) are three delta functions at x ¼ Àt, x ¼ 0, and x ¼ þt. (C) The convolution operation f(x)g(x) results in copying of the three rectangular pulses at x ¼ Àt, x ¼ 0, and x ¼ þt. As with Fourier transforms, the actual mechanics of convolution can rapidly become computationally intensive for a large number of points. Fortunately, many complex procedures can be adequately performed using a variety of digital masks as illustrated in Section VI.C.C. Digital Masks as Convolution Filters For many purposes, the appropriate digital mask can be used to extract features from images. The convolution filter, acting as a selection function g(x), can be used to modify images in a particular fashion. Convolution filters reas- sign intensities by multiplying the gray value of each pixel in the image by the corresponding values in the digital mask and then summing all the values; the resultant is then assigned to the center pixel of the new image and the operation is then repeated for every pixel in the image (Fig. 17). Convolution filters can vary in size (i.e., 3 Â 3, 5 Â 5, 7 Â 7, and so on) depending on the type of filter chosen and the relative weight that is required from neighboring values from the center pixel.
  24. 24. 308 Richard A. Cardullo and Edward H. HinchcliVe Fig. 17 Performing convolutions using a digital mask. The convolution mask is applied to each pixel in the image. The value assigned to the central pixel results from multiplying each element in the mask by the gray value in the corresponding image, summing the result, and assigning the value to the corresponding pixel in a new image buVer. The operation is repeated for every pixel resulting in the processed image. Or diVerent operations, a scalar multiplier and/or oVset may be needed. For example, consider a simple 3 Â 3 convolution filter, which has the form: 1/9 1/9 1/9 1/9 1/9 1/9 1/9 1/9 1/9
  25. 25. 14. Digital Manipulation of Brightfield and Fluorescence Images 309 Applied to a pixel with an intensity of 128 and surrounded by other intensity values as follows: 123 62 97 237 128 6 19 23 124 The gray value in the processed image at that pixel, therefore, would have a new value of 1/9(123 þ 62 þ 97 þ 237 þ 128 þ 6 þ 19 þ 2 þ 124) ¼ 819/9 ¼ 91. Note that this convolution filter is simply an averaging filter identical to the operation described in Section IV (in contrast, a median filter would have returned a value of 128). A 5 Â 5 averaging filter would simply be a mask, which contains 1/25 in each pixel whereas a 7 Â 7 averaging filter would contain 1/49 in each pixel. Since the speed of processing decreases with the size of the digital mask, the most frequently used filters are 3 Â 3 masks. In practice, the values found in the digital masks tend to be integer values with a divisor that can vary depending on the desired operation. In addition, because many operations can lead to resultant values, which are negative (since the values in the convolution filter can be negative), oVset values are often used to prevent this from occurring. In the example of the averaging filter, the values in the kernel would be: 1 1 1 1 1 1 1 1 1 with a divisor value of 9 and an oVset of zero. In general, for an 8-bit image, divisors and oVsets are chosen so that all processed values following the convolu- tion fall between 0 and 255. Understanding the nature of convolution filters is absolutely necessary when using the microscope as a quantitative tool. User-defined convolution filters can be used to extract information specific for a particular application. When begin- ning to use these filters, it is important to have a set of standards, which the filters can be applied to in order to see if the desired eVect has been achieved. In general, the best test objects for convolution filters are simple geometric objects such as squares, grids, isosceles and equilateral triangles, circles, and so on. Many com- mercially available graphics packages provide such test objects in a variety of graphics formats. Examples of some widely used convolution masks are given in the following sections.
  26. 26. 310 Richard A. Cardullo and Edward H. HinchcliVe1. Point Detection in a Uniform Field Assume that an image consists of a series of grains on a constant background (e.g., a dark-field image of a cellular autoradiogram). The following 3 Â 3 mask is designed to detect these points: À1 À1 À1 À1 þ8 À1 À1 À1 À1 When the mask encounters a uniform background, then the gray values in the processed center pixel will be zero. If, on the other hand, a value above the constant background is encountered, then its value will be amplified above that background and a high-contrast image will result.2. Line Detection in a Uniform Field Similar to the point mask in the previous example, a number of line masks can be used to detect sharp, orthogonal edges in an image. These line masks can be used alone or in tandem to detect horizontal, vertical, or diagonal edges in an image. Horizontal and vertical line masks are represented as: À1 À1 À1 þ2 þ2 þ2 À1 À1 À1 À1 þ2 À1 À1 þ2 À1 À1 þ2 À1 whereas, diagonal line masks are given as: À1 À1 þ2 À1 þ2 À1 þ2 À1 À1 þ2 À1 À1 À1 þ2 À1 À1 À1 þ2
  27. 27. 14. Digital Manipulation of Brightfield and Fluorescence Images 311 In any line mask, the direction of nonpositive values used reflects the direction of the line detected. When choosing the type of line mask to be utilized, the user must a priori know the directions of the edges to be enhanced.3. Edge Detection-Computing Gradients Of course, lines and points are seldom encountered in natures and another method for detecting edges would be desirable. By far, the most useful edge detection procedure is one that picks up any inflection point in intensity. This is best achieved by using gradient operators, which take the first derivative of light intensity in both the x- and y-directions. One type of gradient convolution filters, which are often used, is the Sobel filter. An example of a Sobel filter, which calculates horizontal edges, is the Sobel North filter expressed as the following 3 Â 3 kernel: þ1 þ2 þ1 0 0 0 À1 À2 À1 This filter is generally not used alone, but is instead used along with the Sobel East filter, which is used to detect vertical edges in an image. The 3 Â 3 kernel for this filter is: À1 0 þ1 À2 0 þ2 À1 0 þ1 These two Sobel filters can be used to calculate both the angle of edges in an image and the relative steepness of intensity (i.e., the derivative of intensity with respect to position) of that image. The so-called Sobel Angle filter returns arctangent of the ratio of the resultant Sobel North filtered pixel value to the Sobel East filtered pixel value while the Sobel Magnitude filter calculates a resultant value from the square root of the sum of the squares of the Sobel North and Sobel East values. In addition to Sobel filters, a number of diVerent gradient filters can be used (specifically Prewitt or Roberts gradient filters) depending on the specific applica- tion. Figure 18 shows the design and outlines the basic properties of these filters, and Fig. 19 shows the eVects of these filters on a fluorescence micrograph.
  28. 28. 312 Richard A. Cardullo and Edward H. HinchcliVe Name Kernels Uses −1 +1 +1 Detects the vertical edges of Gradient −1 2 +1 objects in an image. −1 +1 +1 North detects horizontal edges; East detects vertical edges. North and East +1 +2 +1 −1 0 +1 used to calculate Sobel Angle and Sobel 0 0 0 −2 0 +2 Sobel Magnitude (see test). Filters should not be used independently; if −1 −2 −1 −1 0 +1 horizontal or vertical detection is desired, use Prewitt. North East +1 +1 +1 −1 0 +1 North detects horizontal edges; Prewitt 0 0 0 −1 0 +1 East detects vertical edges. −1 −1 −1 −1 0 +1 North East Northeast detects diagonal 0 1 1 0 edges from top-left to bottom- Roberts right; Northwest detects −1 0 0 −1 diagonal edges from top-right to Northeast Northwest bottom-left. Fig. 18 DiVerent 3 Â 3 gradient filters used in imaging. Shown are four diVerent gradient operators and their common uses in microscopy and imaging.4. Laplacian Filters Laplacian operators calculate the second derivative of intensity with respect to position and are useful for determining whether a pixel is on the dark side or light side of an edge. Specifically, the Laplace-4 convolution filter, given as: 0 À1 0 À1 þ4 À1 0 À1 0 detects the light and dark sides of an edge in an image. Because of its sensitivity to noise, this convolution mask is seldom used by itself as an edge detector. In order to keep all values of the processed image within 8 bits and positive, a divisor of 8 and an oVset value of 128 are often employed.
  29. 29. 14. Digital Manipulation of Brightfield and Fluorescence Images 313 Fig. 19 DiVerent filters applied to a fluorescence image of a dividing mammalian cell. Inverse contrast LUT, gradient filter, Laplacian filter, Sobel filter. The point detection filter shown earlier is also a kind of Laplace filter (known as the Laplace-8 filter). This filter uses a divisor value of 16 and an oVset value of 128. Unlike the Laplace-4 filter, which only enhances edges, the Laplace-8 filter enhances edges and other features of the object. VII. Conclusions The judicious choice of image-processing routines can greatly enhance an image and can extract features, which are not otherwise possible. When applying digital manipulations to an image, it is imperative to understand the routines that are being employed and to make use of well-designed standards when testing them out. With the advent of high-speed digital detectors and computers, near real-time processing involving moderately complicated routines is now possible.
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