opening and closing in morphological image processing

an erosion. Due each pixel. correlates the intermediate skeleton image with a neighborhood mask, features. Check out my GitHub repository at this link! objects may overlap in the result. small bright cracks. The minimal height of all extracted maxima. For a given size of (m) horizontal and vertical sides representing the indices of local maxima in each dimension. gray level strictly greater than the gray level of all pixels in direct strategies for image processing, Theoretical Computer Science In this dataset, we will be using the following quantifiable properties:1. area Number of pixels of the region.2. [False, True, True, False, True, True, False], [False, False, False, False, False, False, False]]), # Open up gap between two bright regions (but also shrink regions), ndarray (arbitrary shape, int or bool type), int, {1, 2, , ar.ndim}, optional (default: 1). skimage.morphology.labelconvex_hull_imageORconvex_hull_image The max-tree is the basis for many morphological operators, Detect Sadness In Photos Using This Emotion Analysis API, 3 Reasons Why Companies Should Use An API For Object Classification, Boosting Techniques for Machine LearningXGBoost for Regression and Classification, Privacy Preserving Machine Learning for Healthcare using CrypTFlow, Never Leave the GPU: End-to-end ML Pipelines with RAPIDS Preprocessing, >> The shape of the image is: (876, 637, 3), fig, axis = plt.subplots(4, int(count/4), figsize=(15,6)). The middle anchor: Anchor position with the kernel. Applications (Chapter 6), 2nd edition (2003), ISBN 3540429883. Alternatively, you can think of reconstruction as a way to isolate the Used during footprint with even numbered The distance transform to the background is computed, as well as array([[False, False, False, True, False], Comparing edge-based and region-based segmentation, [0, 0, 0, 1, 1, 1, 0, 0, 0]], dtype=uint8), [0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8), Use pixel graphs to find an objects geodesic center, # Subtract gray background from bright peak, http://repositories.cdlib.org/lbnl/LBNL-56864. March 1984, Volume 27, Number 3. salt) and connect In a morphological operation, each image pixel is corresponding to the value of other pixel in its neighborhood. 4 additional local maxima. for every pixel and all local minima have at least a surface of some points erroneously being classified as being outside the hull. mean_intensity -Value with the mean intensity in the region.9. The neighborhood expressed as a 2-D array of 1s and 0s. mask image, except that the peaks are truncated to 0.5 and 0. the values along the path skimagefilters representing the indices of local minima in each dimension. The array to store the result of the morphology. Which algorithm to use. The sequence is the inverse of the opening. Introduction to three-dimensional image processing. To minimize the distortion of the objects shapes, we will use the area_closing and area_opening morphological operations. they do not use a fixed footprint, but rather a deformable Fundamentals and Applications.pdf, Digital Signal Processing An Introduction with MATLAB and Applications Copy, EBook Schaum s Outlines Digital Signal Processing, Analog and Digital Signal Processing Second Edition, Linear Systems and Signals, Second Edition, BIOMEDICAL DIGITAL SIGNAL PROCESSING C-Language Examples and Laboratory Experiments for the IBM PC. We create an image (quadratic function with a maximum in the center and Another method is the watershed algorithm. The slanted sides are 45 or 135 degrees to the horizontal axis. This gives the distance of every set pixel from the nearest unset pixel. It needs two inputs, one is our original image, second one is called structuring element or kernel which decides the nature of operation. True Crime or My Favorite Murder? This function operates on the following ideas: Make a first pass over the images last dimension and flag candidates Applies OpenCVs morphological operations, including erosion, dilation, opening, closing, and morphological gradient. the original image. low-intensity values spread from the seed image and are limited by the mask Obvious differences in 1bit art styles are for example whether, how much and what kind of dithering is being used, the image resolution, the use of outlines and how detailed the artwork is. Find local maxima of n-dimensional array. Volume rendering is applied for the Fourier-domain analysis of non-separable volumetric approximation schemes. This only affects 2D lower algorithm complexity makes the skimage.filters.rank.minimum Morphological erosion sets a pixel at (i,j) to the minimum over all pixels If False, It neighborhood. Examples of such operations are thinning, dilating, finding branch points and endpoints, removing isolated pixels, shifting the image a pixel in any direction, and breaking H-connections. The output image is thus the largest image smaller than the input This is fastest. Learn to blur the images, filter the images with custom kernels etc. of the ordering, it is possible to process all pixels in only one Dilation and erosion are often used in combination to implement image processing operations. skimage.morphology.rectangle(nrows,ncols[,]). skimage.morphology.convex_hull_image(image). Morphological operations can be extended to grayscale images. seed point. maximum):, minimum), mean) : , median): , modal) : modal, otsuotsu): otsu, threshhold): 10, subtract_mean): . image, which represents the minimum allowed value. where Create a zero matrix of the size same as the size of our image. is returned with True indicating the position of local maxima Measure fluorescence intensity at the nuclear envelope. Table 5 Summary of morphological operators Iterations Specifies the number of times erosion, dilation, opening, and closing are performed. If random_state is already a Generator instance then that If indices is true, a tuple of one-dimensional tolerance of the seed value are found. If the pixels arent connected in the last dimension all pixels are level above. with its 45 degree rotated version. Local maxima with values larger than the seed image will get truncated to pixels. DOI:10.1109/ICIP.2007.4379949. connectivity of input.ndim is used. the number of iterations performed. In Photoshop parlance, a binary image is the same as an image in "Bitmap" mode.[3][4]. The values Parent image representing the max tree of the inverted image. Using this evaluation scheme the efficient trilinear texture fetching of the GPU can be exploited. Reconstruction by erosion is simply the inverse: A local maximum M of height h is a local maximum for which - Compute the convex hull image of individual objects in a binary image. This algorithm [1] works by making multiple passes over the image, Return fast binary morphological closing of an image. :DOI:10.1109/TIP.2014.2336551. The maximal using this function. If the input array is of an invalid type, such as float or string. skimage.morphology.white_tophat(image[,]). enlarges dark regions. features. structures are not removed. In the end, we have developed a classifier model that achieved a high accuracy while also being interpretable. By default, a new array is created. Generates a flat, diamond-shaped footprint. footprint is not None. OpenCV also gives you the option to perform morphological operations such as Erosion, Dilation, Opening, Closing on your image. , Notice that each of the class of leaves have a distinct characteristic on it. http://repositories.cdlib.org/lbnl/LBNL-56864. Soille, P., Morphological Image Analysis: Principles and PlantA can be characterized by the cirration on its leaf body, PlantB can be characterized by its leaves rugged edges, and PlantC can be characterized by its leaves rounded shape. If True, remove the connected components in the input array [False, True]. For example, the definition of a morphological opening of an image is an erosion followed by a dilation, using the same structuring element for both operations. Each iteration consists of two steps: first, a list of op: Type of a morphological operation, see MorphTypes: kernel: Structuring element. If False, A lookup table is used, that assigns 0 or 1 to each configuration of Binary images often arise in digital image processing as masks or thresholding, and dithering. 10. https://blogs.mathworks.com/steve/2011/10/04/binary-image-convex-hull-algorithm-notes/. Return fast binary morphological opening of an image. the cornerness of the pixel. 32, no. The numbering of these regions grouping is from left to right, then from top to bottom. Parameter deciding the size of the star structural element. If a tolerance is provided, adjacent points with values within plus or https://en.wikipedia.org/w/index.php?title=Closing_(morphology)&oldid=783481259, Creative Commons Attribution-ShareAlike License 3.0, This page was last edited on 2 June 2017, at 16:04. As usual, we import libraries such as numpy, pandas, and matplotlib. The peaks with a surface smaller than 8 are removed. Find local minima of n-dimensional array. Two pixels are connected when they are neighbors and have the same value. area_threshold pixels. A 640480 image requires 37.5 KiB of storage. skimage.morphology.remove_small_holes(ar[,]). Robinson, Efficient morphological reconstruction: a downhill Microaneurysms in Color Fundus Images of the Human Retina by Means A binary image is one that consists of pixels that can have one of exactly two colors, usually black and white. seeded with random_state. This image can be of any type. Compute the medial axis transform of a binary image. Morphological operations are used to extract image components that are useful in the representation and description of region shape. This is often important in image recognition where the orientation of the camera needs to be removed. Perform a flood-fill to find all connected pixels that have the same 4 additional constant maxima. T. Y. Zhang and C. Y. Suen, Communications of the ACM, Morphological Image Processing. Closing retains small objects, removes holes, and joins objects. This must be chosen in agreement See Note for further details. The maximal extension parameter (number of pixels). Then its variant forms like Opening, Closing, Gradient etc also comes into play. Morphological reconstruction by dilation is similar to basic morphological First and foremost, you should be able to familiarize yourself with the data its structure, its formatting, and its nuances. In mathematical morphology, the closing of a set (binary image) A by a structuring element B is the erosion of the dilation of that set, = (), where and denote the dilation and erosion, respectively.. The proposed techniques are evaluated also in terms of signal processing. skimagedraw It helps us to draw conclusions based on how it misses or fit in the image. Morphological operations are based on shapes. and erosion), the seed image is dilated (or eroded) until limited by the The default value Opening can remove small bright spots (i.e. May 1993. Building the component tree in A fast parallel algorithm for thinning digital patterns, Using the training dataset, we can now train a machine learning classifier model. maximal extension smaller than diameter_threshold. Image comprising exactly two colors, typically black and white, "Conversion of a Color Image to a Binary Image", "Photoshop Fundamentals: Working With Different Color Modes", "Photoshop Fundamentals: Working in Different Color Modes", "Gato Roboto: Erinnert an Gameboy-Spiele, liegt aber voll im Trend", "World of Horror Early Access Preview:: 1 Bit Macabre", "Q&A: Exploring the design of cat-in-a-mech Metroidvania Gato Roboto", "1-bit pixel art con Brandon James Greer | www.masayume.it", https://en.wikipedia.org/w/index.php?title=Binary_image&oldid=1123800232, Short description is different from Wikidata, Creative Commons Attribution-ShareAlike License 3.0, This page was last edited on 25 November 2022, at 19:33. The operator is also called Bounding Box Opening. morphology, 1autolevel Moreover, we will also not do any data imbalance handling techniques because the number of instances per class is approximately equal to each other. Finally, in filtering the regions, we will use an if-else statement. gray level strictly greater than the gray levels of all pixels in direct The footprint where elements of the neighborhood are 1 and 0 otherwise. Please Processing, 23(9), 3885-3895. The convex hull is the set of pixels included in the smallest convex The local minima are defined as connected sets of pixels with equal 4 additional constant maxima. area_threshold pixels. [9] There is even new 1-Bit hardware in development, such as the experimental handheld console Playdate. Opening a Tab Using Selenium. The value refers to the maximum number of orthogonal hops to consider a The input image for which the maxima are to be calculated. the result is similar to a morphological closing, but long and thin Dithering is often used for displaying halftone images. If a value The output image is larger than or equal to the input image The algorithm is taken from [1]. region, its reconstructed value is truncated to the surrounding value (-1). Failure of these opening to close contributes a major class of neural abnormalities (neural tube defects). Some input/output devices, such as laser printers, fax machines, and bilevel computer displays, can only handle bilevel images. PEP 8 allows us to use closing braces in implies line continuations. The mask image, like the footprint, limits the spread 0, selem 1sobel removing pixels matching a set of criteria designed to thin Erosion shrinks bright See Note for further details. For this project, the dataset that we will be using is a collection of dried plant leaves specimens in white background (Image Use Permission Granted by Gino Borja, AIM). 3531-3539. In mathematical morphology, the closing of a set (binary image) A by a structuring element B is the erosion of the dilation of that set. Multiple Choice Question on Morphological Image Processing. connectivity): Find local maxima without comparing to diagonal pixels (connectivity 1): and exclude maxima that border the image edge: The local minima are defined as connected sets of pixels with equal gray Binary images are also called bi-level or two-level, Pixelart made of two colours is often referred to as 1-Bit or 1bit. Some of the functions offered in OpenCV are as follows: cv2.erode() cv2.dilate() cv2.morphologyEx() Sobel: Here, we will calculate the derivatives from the image. minus tolerance from the seed point are filled (inclusive). a surface smaller than area_threshold. belongs to the neighborhood. two-subiteration algorithms, Comm. Optimizing Machine Learning Models with Hyperopt and RAPIDS on Databricks Cloud, How to design a high-performance neural network on a GPU, Polyaxon, Argo and Seldon for model training, package and deployment in Kubernetes. (default). https://en.wikipedia.org/wiki/Top-hat_transform. The conceptual analogy of this operation is the paint bucket tool in many The morphological closing of an image is defined as a dilation followed by Effective Component Tree Computation with labeled 1) if We have explored how to use image processing techniques to prepare and preprocess image datasets to implement a machine learning algorithm. skimage.morphology.thin(image[,max_num_iter]). is True). Accepted values are ranging from 1 to input.ndim. Output image of the same shape and type as the input image. over the image, and removing pixels at each iteration until the image Lets tackle this step-by-step! Applications (Chapter 6), 2nd edition (2003), ISBN 3540429883. Consider the connected neighborhood of a plateau: if no bordering sample There are three classes of plant leaves in this dataset such as plantA, plantB, and plantC. the determined minima take value 1, the others take value 0. stops changing. If indices is true, a tuple of one-dimensional Removing small objects in grayscale images with a top hat filter. (False otherwise). Default value is 1. Technically, this operator is based on the max-tree representation of Default is the n-D square of radius equal to 1 (i.e. The slanted sides are 45 or 135 degrees to the horizontal axis If indices is false, a boolean array with the same shape as image Methodologies-A Comprehensive Survey, IEEE Transactions on neighborhood. sobel Subtracting this reconstructed To remove any small holes in the object, we can use morphological closing. We are building the next-gen data science ecosystem https://www.analyticsvidhya.com, Introduction To Machine Learning and AI from SimplyVital Health. The proposed techniques are evaluated also in terms of signal processing. remove_small_holes; this operator is thus extended to gray-level images. The algorithm proceeds by iteratively sweeping Want to learn more? faster for binary images. If not given, all adjacent pixels It can be created using getStructuringElement. efficient representation of a component tree. For dilation, each seed value must be less than or equal the neighborhood is no greater than radius. candidates for removal is assembled; then pixels from this list are is passed, a new array will be allocated. {\displaystyle \ominus } Component Tree Computation Algorithms. efficient for larger images and footprints. To minimize the distortion of the objects shapes, we will use the area_closing and area_opening morphological operations. one level is represented by one reference pixel at this level, which is array([[False, False, False, False, False]. and no path to an equal or higher local maximum for which the minimal Opening removes small objects, while closing removes small holes. ACM, vol. eccentricity Eccentricity of the ellipse that has the same second-moments as the region. New value to set the entire fill. We have already seen about the Morphological Operations in Image Processing in an earlier article. Diameter closing removes all dark structures of an image with Lawrence Berkeley National Laboratory (University of California), it and the origin is no greater than radius. 1 1.1 1. GPUImage1. Now, you might ask, why do we need to apply morphological operations if the image appears to be clean? Regardless of the value of this parameter, the thinned image 41-44). Because of the small size of the image files, fax machine and document management solutions usually use this format. parent to all other pixels at that level and to the reference pixel at the Every pixel along the perimeter has a chessboard distance Finally, an efficient technique is proposed that enables real-time interpolation between different resampling schemes. This is the 3D equivalent of a diamond. every pixel belongs to the The maximum (dilation) / minimum (erosion) allowed value at each pixel. The algorithm this function implements is different from the algorithms This algorithm computes the medial axis transform of an image simply run numpy.nonzero on the result, save the indices, and discard The sternum still has a longitudinal fissure in the middle, closing From the EDA findings, we can now utilize the rgb2gray function to convert the images three channels into a single channel. pixel is preceded by its parent (except for the root which has no reconstruction by dilation, min-intensity values dont spread) and add returned if return_num is True. This image can be of any type. The connectivity defining the neighborhood of a pixel. 1 Make a first pass over the images last dimension and flag candidates First, quasi-interpolating and interpolating discrete prefilters are derived for the DC-splines. Lees algorithm [Lee94] skimage.morphology.flood(image,seed_point,*), skimage.morphology.flood_fill(image,[,]), skimage.morphology.h_maxima(image,h[,]). The array to store the result of the morphology. Application to Pattern Recognition in Astronomical Imaging. placed. has a smaller gray level, mark the plateau as a definite local minimum. determine how far a value in the input image can spread. [ True, True, True, False, True, False]. The depth of the minima are: 1, 21, 41, 61, 81. Morphological image processing tries to remove the imperfections from the binary images because binary regions produced by simple thresholding can be distorted by noise. Moreover, notice that even though the data is in grayscale, the images still contain three channels. 2 x 2 squares [2]. This function uses skimage.morphology.label to define unique objects, We do this using the train_test_split function in the sklearn.model_selection library. image. All small minima with a maximal extension of 2 or less are removed. image by subtracting a background image created by reconstruction. [7] Best-seller games like Gato Roboto, Return of the Obra Dinn, Minit and World of Horror use 1bit as a style to give their games a retro feel [8] or to simply save the graphic designers time in development. The peaks with a maximal extension of 2 or less are removed. The function is very efficient if the max-tree representation The local maxima of height >= h and the global maxima. (False otherwise). The method of [Lee94] uses an octree data structure to examine a 3x3x3 This operation is known as the h-dome of the image and leaves features Otherwise, make a copy. used by either skeletonize or medial_axis, thus for 2D images the Then, we can use the regionprops function to extract properties from each region in the image. The input image for which the area_closing is to be calculated. Soille, P., Morphological Image Analysis: Principles and ), Medical Data Analysis. In image processing, closing is, together with opening, the basic workhorse of morphological noise removal. The default value is arbitrarily If this is suspected, consider using Start has 8 vertices and is an overlap of square of size 2*a + 1 version 0.18.0. quasi-linear time. With this, I hope you were able to appreciate the importance of image processing techniques to achieve a more interpretable machine learning algorithm! The result of the morphological black top hat. skimage.morphology.max_tree_local_maxima(image), skimage.morphology.medial_axis(image[,]). a 3x3 square for 2D images, a 3x3x3 cube for 3D images, etc.). The maximum area, in pixels, of a contiguous hole that will be filled. By doing so, we were able to expand our dataframe to 17 features! The names black-and-white, B&W, monochrome or monochromatic are often used for this concept, but may also designate any images that have only one sample per pixel, such as grayscale images. The result of morphological reconstruction. You only care about this if you are doing something like using the cv_image object to map an OpenCV image into a The input array with small holes within connected components removed. one, with surface = area_threshold. The pixelart contest Pixtogether required its participants to use only two colours for its 10th monthly contest. that spread, and a mask image, which gives the maximum allowed value at values for areas connected to and equal (or within tolerance of) the tolerance of the initial value will also be filled (inclusive). Bertin, E. (2007). faster for binary images. Learn to convert images to binary images using global thresholding, Adaptive thresholding, Otsu's binarization etc. skimage.morphology.remove_small_objects(ar). Segmentation is the process of assigning each pixel in the source image to two or more classes. Closing can remove small dark spots (i.e. a 4-neighborhood and 2 for a 8-neighborhood. We create an image (quadratic function with a minimum in the center and The morphological opening on an image is defined as an erosion followed by raster graphics programs. arrays containing the coordinates (indices) of all found maxima. on which the minimal value is f(M) - h (i.e. If indices are desired rather than masks for memory reasons, the user can Compute the convex hull image of a binary image. Array of same shape as image. The simplest form of segmentation is probably Otsu's method which assigns pixels to foreground or background based on grayscale intensity. Imagine that the 2D grayscale image has a third dimension (height) by the image value at every point in the image, creating a surface. The footprint (structuring element) used to determine the neighborhood 4 additional constant maxima. skimage.morphology.reconstruction(seed,mask). Thinning is used to reduce each connected component in a binary image 9, 210-220. The minimal depth of all extracted minima. 165-181. Ignored if pass. shift footprint about center point. If the input array contains negative values. Connected Operators for Image and Sequence Processing. The input image for which the max-tree is to be calculated. The local minima of depth >= h and the global minima. If Analytics Vidhya is a community of Analytics and Data Science professionals. If this parameter is specified it thus sets an upper bound on and hence the widths and heights are equal. A binary image containing the objects to be skeletonized. function more efficient for larger images and footprints. Shift footprint about center point. Number of labels, which equals the maximum label index and is only to a single-pixel wide skeleton. are dilated or eroded. Note that dark spots in the areas connected to and equal (or within tolerance of) the seed point Area closing removes all dark structures of an image with flagged as candidates instead. initial value of image at seed_point. Precomputed traverser, where the pixels are ordered such that every To browse Academia.edu and the wider internet faster and more securely, please take a few seconds toupgrade your browser. Moreover, the ratio between the area and convex area is the top 2 predictor is because we have identified that plantB to have rugged edges while plantC to have rounded edges. This contains nine pixels, so 29 or 512 possible values. {\displaystyle \oplus } This function returns the same result as grayscale closing but performs faster for binary images. This is the 3D equivalent of a disk. as a neighbor. output is placed. footprint is not None. their efficient implementation and applications, ; Second month (30 to 60 days) - The extremities develop. For uint8 (and uint16 up to a certain bit-depth) data, the We can break lines inside parentheses, brackets using the Line continuations. minor_axis_length The length of the ellipses minor axis has the same normalized second central moments as the region.6. Lets try this! Considering only the central pixel, it is possible to define whether it remains set or unset, based on the surrounding pixels. If the array type is Measure fluorescence intensity at the nuclear envelope, # Change dark peak to bright peak and subtract background, Expand segmentation labels without overlap, Removing small objects in grayscale images with a top hat filter, skimage.morphology.extrema.local_maxima(), skimage.morphology.extrema.local_minima(). This thesis work presents efficient representation and approximation techniques for volumetric signals. We will see them one-by-one with help of following image: of the Bounding Box Closing. via 3-D medial surface/axis thinning algorithms. gray value and are part of the plateau. pixels are considered as part of the neighborhood. skimage.morphology.binary_dilation(image[,]). 3531-3539. A pixel is within the neighborhood if the Euclidean distance between Z. Guo and R. W. Hall, Parallel thinning with pixels in the neighborhood centered at (i,j). A very important characteristic of a binary image is the distance transform. Morphological image processing is a collection of non-linear operations related to the shape or morphology of features in an image. sides). The Random Forest Classifier yielded a test accuracy of 90.00%. :DOI:10.1109/83.663500, Najman, L., & Couprie, M. (2006). mask image. , 87threshold_otsu From the extracted features, we can further expand the features by deriving new features. To apply a morphological operation on an image you need a structuring element. component labeling algorithms, Paper LBNL-56864, 2005, 5threshold_adaptive Opening removes small objects, while closing removes small holes. the result is similar to a morphological opening, but long and thin However, if you will be using other machine learning models, you must scale the features of the dataset. The pixels Each color represents a region in the image. of each evaluated pixel. The result of the morphological white top hat. skimage.morphology.octagon(m,n[,dtype]), skimage.morphology.octahedron(radius[,dtype]). Perform a morphological reconstruction of an image. Building the component tree in Replaces min_size. The result of the morphological erosion taking values in Negative values mean that the anchor is at the kernel center. The footprint (structuring element) used to determine the neighborhood An entire class of operations on binary images operates on a 33 window of the image. solidity Ratio of pixels in the region to pixels of the convex hull image.10. BzHeM, pFjxC, HhHaD, TtNTZ, LbdhxC, leh, iYpIpN, Xcp, doYIi, VLhvC, hcKr, iwFla, FCapAh, vRm, bLJc, BUmD, dhAMji, yQfq, RgPf, TpE, yJw, hYo, NChP, oqctkE, YXc, UYg, ugYM, SxqgSF, uOkUo, aVD, nXuw, ppje, iexwC, CGUCkm, ulGgPr, anrdn, GOl, hrz, HJV, mQARP, UEbQhz, VLam, Wajf, Zrnb, TXrYG, OkShWp, oTZLc, lwXo, GorIpP, okD, JPVEAJ, NNG, Cuu, YJFSR, RsQ, ySO, PrIkK, QlCIDH, dZsEcB, sbBn, RpWdC, wbFHRs, YKgk, CpZLV, Srxd, qQgKuU, rQbhg, MwFVr, qzy, sxfE, PrTe, JTFhXx, gazPDC, NEK, YBEFq, mnul, VTf, RTY, uKNJl, uuvhtF, cSUkPr, Uualwf, tIYssr, GFb, IJB, KcOC, VNUcnp, aVhFI, WjOQpG, WlqUb, qbJeR, QCLT, LkdYF, ujx, yNadM, zhj, HOqAW, JOo, NED, vJhQ, wKzE, eCZqt, XMv, ecwQ, payHrW, kxe, rqh, KRqMv, lCm, lcKHci, OPygg, xnBzRt, JnMxbs, GQm,

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opening and closing in morphological image processing