Digimizer Copyright MedCalc Software bvba MedCalc Software Acacialaan Ostend Belgium

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2 MedCalc Software bvba. All rights reserved. No part of this package, neither the documentation nor the software may be reproduced, stored in a retrieval system, or transmitted in any form by electronic, mechanical, photocopying, or any other means without the prior written permission of the publisher. The author and the publisher make no representations or warrants with respect to the software and the documentation and specifically disclaim any implied warranties of fitness for any particular use. Microsoft, Excel, Windows and Windows Vista are trademarks or registered trademarks of Microsoft Corporation in the United States and/or other countries. Digimizer and MedCalc are registered trademarks. Version 5.1 Digimizer Copyright MedCalc Software bvba MedCalc Software Acacialaan Ostend Belgium info@medcalc.org

3 Contents Get started... 1 Software installation... 1 Digimizer application window... 2 The Measurements list and the Digimizer image file format DGZ... 3 Examples... 4 How to straighten an image... 4 How to calibrate measurements... 4 How to edit measurement objects... 5 How to select measurement objects... 5 Automatic measurement of leaf area... 6 Toolbar File controls Edit controls Rotate & Flip controls - Crop control Measurements toolbar Measurements tools Select tool Lock tool Unit tool Length tool Middle tool Angle tool Perpendicular line tool Path tool Area tool Center tool Circle tool Rectangle tool Marker/Counter tool Magic contour tool Color selection tool Brightness & Contrast controls Zoom controls Menu overview File menu Open Image Close New Image from Clipboard Save Save as Select Scanner Acquire Image from Scanner Grab Image from Camera Print Exit File - Measurements List menu New Open Save Save As Export i

4 Edit menu Undo Cut Copy Paste Delete Duplicate Select all View menu Measurements List Statistics Measurements List Columns Grid Zoom to Fit Zoom In Zoom Out Format menu Resize Crop Rotate Flip Reset Calibration Image menu Contrast Auto Fix Stretch Histogram Background Correction Despeckle Convert to Grayscale Invert Negative Adjust colors Selective color brightness Sharpen Filters Canny Edge Detector Emboss Filter Arithmetic Mean Filter Geometric Mean Filter Harmonic Mean Filter Median Filter Maximum Filter Minimum Filter Midpoint Filter Range Filter Yp Mean Filter Binary menu Binarization Overlay Binary Image Hide Binary Layer Morphological Dilate Morphological Erode Morphological Close Morphological Open Noise Reduction Analyze Objects Import Binary Layer Tools menu Scripts Edit script Options ii

5 Window menu Reset Window Layout Help menu Digimizer help What's new? About Digimizer Index iii

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7 Get started Software installation System requirements To run the Digimizer program you need a PC with Windows XP or later, with at least 1 GB RAM and about 8 Megabyte free space on the hard disk. Software installation If you have downloaded the software from the Internet, you should locate the setup file digimizersetup.exe on your hard disk and execute (double-click) it. If you have a program CD, locate the setup file digimizersetup.exe on the CD and execute it. Next follow the instructions of the installation procedure To setup Digimizer you must be logged on to your computer with administrator privileges. The digimizersetup.exe file is suitable for new installations as well as software updates. If you have previously installed Digimizer, you must close any open (running) copy of Digimizer first. When installation is complete, you start Digimizer by clicking the Start button and point to Programs, next click Digimizer. Sample data At first run, Digimizer creates a folder named "Digimizer" with a subfolder "Sample files" in the "(My) Documents)" map. The "Sample Images" folder contains the following sample files: leafs.png X-ray Dog.jpg What's new If you are already familiar with Digimizer, you can read about the latest changes and additions in Digimizer by selecting the option What's new in the Digimizer Help menu. Updated versions of the manual in PDF format can be downloaded from the Digimizer web site 1

8 Digimizer application window The different parts of the Digimizer application window are indicated in the following figure. Digimizer menu In the menu you select the different commands and options. See p. 22 for a complete overview of all menu commands. Toolbar The toolbar contains buttons for the most common commands. Inactive buttons are displayed in gray. When you hover the mouse over an active button, a short description of the corresponding command is displayed in a small popup window. See p. 10 for a short description for all buttons on the toolbar. Measurement tools The measurement tools toolbar contains the different tools for manual measurements in the image. For an overview of all measurements tools, see p. 11. Measurements list The measurements list contains the different measurements performed in one or more images. 2

9 Only the parameters selected in the Measurements List Columns options box (p. 35) are displayed in the Measurements list window. To close the Measurements list window, click the button When the Measurements list window is not visible, select the command View measurements list (p. 29). Click the button to obtain the following shortcut menu: New: starts a new measurements list. Open: opens an existing Measurements List file. Save: save the measurements list as a file. Save as: saves the measurements list as a new file. Export: allows to export the measurements list as an Excel spreadsheet file, or as a MedCalc file for statistical analysis. Print: print the information displayed in the Measurements list window Columns: select the columns visible in the Measurements list window (see p. 30). Statistics The statistics window displays summary statistics for the different measurements that are displayed in the measurements list. To close the Statistics window, click the button When the Statistics window is not visible, select the View statistics command (p. 30). Click the button to obtain the following shortcut menu: Select Print to print the information displayed in the Statistics window. The Measurements list and the Digimizer image file format DGZ In Digimizer, you can save image in a special file format with file extension DGZ. The files in this format do not only contain the image in a compressed format (without quality loss), but also the measurements performed in this image. When you re-open such file the measurements are added if not already there to the current measurements list, and you can add, delete or modify the measurements. All measurements performed in Digimizer have a global unique identifier number. These identifiers prevent that re-opening the file results in duplicates in the measurements list. 3

10 Examples How to straighten an image To straighten an image: Click the Straighten button. Identify a line in the image that should be straight (vertically or horizontally), and then click one end of that line. Click the other end of the line. The image is straightened. Example Before: Identify straight line: The image is rotated: How to calibrate measurements Click the Unit tool. Identify a line in the image of which the length is known, and then click one end of that line. Click the other end of the line. Enter the real length and select the unit in the dialog box that appears. Click OK. 4

11 How to edit measurement objects How to move points of a measurement object Click and drag a point of the object to a new location. Other modifications of a measurement object Right-click on an object. Make your selection in the popup menu. How to select measurement objects First click the Select button. To select a single object: Click on the object in the image. To select more objects: Click on different objects while holding down the Ctrl key. - or - Drag a rectangle over the different objects. To unselect objects: Click on the objects while holding down the Ctrl key. - or - Drag a rectangle over the objects while holding down the Ctrl key. 5

12 Automatic measurement of leaf area Open image file leafs.png, which is present in the Digimizer\Sample Images subfolder in the My Documents folder. Select Contrast autofix in the Image menu. This will automatically maximize the contrast in the image. The image contains a ruler which we will use to calibrate our measurements. Select the Zoom in tool. Drag a rectangle over the ruler so it is enlarged. Select the Unit tool. Click on the small vertical line above the value 0 and next click on the line above the value 10. A dialog box is displayed in which we enter the real length of the unit line: 10 cm. Click the Zoom to fit tool. Select Binarization in the Binary menu. The following dialog box is displayed: 6

13 The dialog box displays a histogram of gray levels. A red line indicates the default threshold value. Click Preview. All gray levels below the threshold value will become red (indicating an object), those above white (indicating background). Click OK to accept the threshold value. Select Analyze Objects in the Binary menu. Complete the dialog box as follows (a minimum area of 3 cm² is required for an object to be identified as a leaf): 7

14 The leafs are now outlined. The characteristics of the 6 leafs are displayed in the measurements list, and the mean area and perimeter are displayed in the statistics window: 8

15 Select Hide Binary layer in the Binary menu so you can judge how well the areas fit the leafs. 9

16 Toolbar File controls Open image file (p. 22) Save image (p. 23) Print (p. 24) Edit controls Cut (p. 27) Copy (p. 27) Paste (p. 28) Undo (p. 27) Rotate & Flip controls - Crop control Rotate counterclockwise (p. 34) Rotate clockwise (p. 34) Flip horizontally (p. 35) Flip vertically (p. 35) Straighten image (p. 4) Crop image (p. 33) 10

17 Measurements toolbar You can measure objects in the image using any of the following Measurement tools: Select (p. 12) Allows to select existing measurement objects in the image. Lock tool (p. 12) When the lock is Open, the program returns to Select mode after performing a measurement using any of the tools below. Close the lock when you need to perform several measurements with the same tool. Unit (p. 12) Draw line (click two points) to define the unit of measurement. Length (p. 13) Draw line to measure a length or distance. Middle (p. 13) Draw line and mark middle point. Angle (p. 14) Click 3 points to measure an angle. Perpendicular line (p. 14) First click 2 points to draw a line. Next click a 3rd point to draw a second line perpendicular on the first line. The middle point of the second line is shown. Path (p. 15) Click several points to obtain a path and calculate its total length. Area (p. 16) Click several points to obtain an area (closed path) and calculate its surface area and perimeter. Center (p. 17) Click several points and find their common center assuming they form a circle. Circle (p. 17) Click a point to define the circle, move the mouse to the center of the circle and click. Rectangle (p. 18) Measures a rectangle. Marker/Counter (p. 19) Click in the image to place a marker. Marker/Counter (p. 19) Click in the image to place a marker. Magic contour (p. 19) Finds the contour of objects automatically. Color selection tool (p. 20) Select color for measurement objects. 11

18 Measurements tools Select tool Button Use Select a measurement object by clicking on its outline. To select multiple objects: place the mouse pointer just outside (not on) the first object you want to select; hold down the left mouse button and drag the mouse pointer over the other objects; or click different objects whilst pressing the Ctrl key; or press Ctrl+A to select all objects. When multiple objects are selected, you can unselect one by clicking it whilst pressing the Ctrl key. Lock tool Buttons Use When the lock is Open, the program returns to Select mode after performing a measurement using any of the Measurement tools. Close the lock when you need to perform several measurements with the same tool. Unit tool Button Use Use this tool to calibrate your measurements. Click the Unit tool. Identify a line in the image of which the length is known, and then click one end of that line. Click the other end of the line. Enter the real length and select the unit in the dialog box that appears. 12

19 Click OK. The length (in pixels) is displayed in the Measurements list window. When the option Show result after finalizing measurement is selected, then the length is displayed in a small window next to the object. After you have defined the unit, all previous measurements are recalculated. Tip A default calibration can be defined in the options box (p. 62). Length tool Button Use To measure a length or a distance: click on one side of the object or distance to measure click on the other site of the object or distance to measure Tip: while you are moving the mouse to the second position, length and angles are displayed in the status bar at the bottom of the Digimizer window. Measurements The length is displayed in the Measurements list window (*). When the option Show result after finalizing measurement is selected, then the length is displayed in a small window next to the object. Summary statistics for all lengths measured with the Length tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. Middle tool Button Use Use this tool to measure a length or a distance, and mark the middle point: click on one side of the object or total distance to measure 13

20 click on the other site of the object or total distance to measure Tip: while you are moving the mouse to the second position, total and half length and angles are displayed in the status bar at the bottom of the Digimizer window. Measurements The total length is displayed in the Measurements list window (*). When the option Show result after finalizing measurement is selected, then the length and half length are displayed in a small window next to the object. Summary statistics for all total lengths measured with the Middle tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. Angle tool Button Use Click 3 points to measure the angle alpha: Tip: while you are moving the mouse to the second and third position, lengths and angles are displayed in the status bar at the bottom of the Digimizer window. Measurements The angle is displayed in the Measurements list window (*). When the option Show result after finalizing measurement is selected, then the angle is displayed in a small window next to the object. Summary statistics for all angles measured with the Angle tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. Perpendicular line tool Button Use First click 2 points to draw a line. Next click a 3rd point to draw a second line perpendicular on the first line. The middle point of the second line is shown. 14

21 Tip: while you are moving the mouse to the second and third position, lengths and angles are displayed in the status bar at the bottom of the Digimizer window. Measurements The total length and angle are displayed in the Measurements list window (*). When the option Show result after finalizing measurement is selected, then the total length and angle are displayed in a small window next to the object. Summary statistics for all lengths and angles measured with the Perpendicular line tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. Path tool Button Use Click several points to obtain a path and calculate its total length. Double-click the last point (point 5 in the example) to finish. Tips To undo a mouse click, press the Esc key. "Lasso" function: when using the path or area tools, the program will "sample" points when you press the Ctrl key whilst moving the mouse. While you are moving the mouse to the next position, lengths and angles are displayed in the status bar at the bottom of the Digimizer window. Measurements The total length is displayed in the Measurements list window (*). When the option Show result after finalizing measurement is selected, then the total length is displayed in a small window next to the object. Summary statistics for all lengths measured with the Path tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. 15

22 Area tool Button Use Click several points to obtain an area (closed path). Double-click the last point (point 7 in the example) to close the path. Tips To undo a mouse click, press the Esc key. "Lasso" function: when using the path or area tools, the program will "sample" points when you press the Ctrl key whilst moving the mouse. While you are moving the mouse to the next position, lengths and angles are displayed in the status bar at the bottom of the Digimizer window. Measurements The surface area, perimeter, length, width, centroid (geometric center), roundness, average intensity and hue are displayed in the Measurements list window (*). Roundness is defined by (4*PI*Area) / (Perimeter*Perimeter) and is a number between 0 and 1. Values closer to 1 indicate a more 'round' object. A circle has a roundness of 1. Definition of length and width: Length is maximum distance between any 2 points on the object outline. Width is the sum of the two maximum perpendicular distances between length-axis and any point on the object outline, on both sides of the length-axis. When the option Show result after finalizing measurement is selected, then the area and perimeter are displayed in a small window next to the object. Summary statistics for all areas, perimeters, lengths, widths and average intensities measured with the Area tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. 16

23 Center tool Button Use Click several points and find their common center assuming they form a circle. Double-click the last point (point 5 in the example) to finish. Tips To undo a mouse click, press the Esc key. "Lasso" function: when using this tool, the program will "sample" points when you press the Ctrl key whilst moving the mouse. While you are moving the mouse to the next position, lengths and angles are displayed in the status bar at the bottom of the Digimizer window. Measurements The radius is displayed in the Measurements list window (*). When the option Show result after finalizing measurement is selected, then the radius is displayed in a small window next to the object. Summary statistics for all radiuses measured with the Center tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. Circle tool Button Use To measure a circle: click one point on the circle move the mouse to the center of the circle and click 17

24 Tips While you are moving the mouse to the center position, radius and angles are displayed in the status bar at the bottom of the Digimizer window. As an option, quadrants can be displayed in the circle (see Options, p. 62) Measurements The radius, perimeter, area, average intensity and hue are displayed in the Measurements list window (*). When the option Show result after finalizing measurement is selected, then the radius, diameter, perimeter and area are displayed in a small window next to the object. Summary statistics for all radiuses, areas, perimeters and average intensities measured with the Circle tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. Rectangle tool Button Use To measure a rectangular shape: click one corner point of the rectangle move the mouse to the opposite corner point of the rectangle and click Measurements The area, perimeter, width, height, average intensity and hue are displayed in the Measurements list window (*). Width and height are measured on the vertical and horizontal axes respectively. When the option Show result after finalizing measurement is selected, then the perimeter, area, width and height are displayed in a small window next to the object. Summary statistics for all areas, perimeters, widths, lengths, and average intensities measured with the Rectangle tool are displayed in the Statistics window. * Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. 18

25 Marker/Counter tool Buttons Use Click in the image to place a marker. To count objects: click on the Lock tool so it shows the locked state select one of the two marker tools or click in the image on the different objects the number of objects is displayed in the Statistics window Measurements Digimizer counts the number of each marker. The totals are displayed in the Statistics window. Magic contour tool Button Use Finds the contour of objects automatically. Select the magic contour control Click inside the object (or drag a 'sampling' rectangle inside the object for increased precision) The program locates the contour of the object If the contour does not reach the actual border of the object: click on the contour and delete it, increase the tolerance and try again. If the contour goes beyond the actual border of the object: click on the contour and delete it, decrease the tolerance and try again. Measurements The surface area, perimeter, length, width and average intensity are displayed in the Measurements list window (*). When the option Show result after finalizing measurement is selected, then the area and perimeter are displayed in a small window next to the object. 19

26 Summary statistics for all areas, perimeters, lengths, widths and average intensities measured with the Magic contour tool are displayed together with those of other Areas in the Statistics window. Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in the Measurements list window. Color selection tool Button Use Select color for measurement objects. To change the color of existing objects, select these objects first and next select the new color. Brightness & Contrast controls Brightness Contrast To change the image brightness: enter a brightness value in the range -100 to 100 and press Enter, - or - use the up-down control to increase or decrease the brightness. To change the image contrast: enter a contrast value in the range -100 to 100 and press Enter, - or - use the up-down control to increase or decrease the contrast. Example Before: Increased brightness: Increased brightness and contrast: 20

27 Related items Contrast Auto Fix (p. 36) Stretch Histogram (p. 36) Zoom controls Zoom factor To change the zoom factor: enter the zoom factor in the range 1 to 2000 and press Enter, - or - use the up-down control to increase or decrease the zoom factor. Zoom in Click in the image to increase the zoom factor and show more detail. Zoom out Click in the image to decrease the zoom factor and show less detail. Fit Adjusts the zoom so that the image fits inside the window. Drag Move the image inside the window. Tip To zoom into a specific area: click a starting point and then move the mouse to drag the rectangle over the area of interest. Note Zooming only magnifies the image on your screen; it does not change the physical size of the picture. 21

28 Menu overview File menu Open Image File Open Image Loads an image file from disk. Digimizer can read image files in the following formats: Digimizer image format (*.dgz) JPEG Interchange format (*.jpg; *.jpeg) Tagged Image File Format (*.tif) Windows bitmap (*.bmp) Graphic Interchange Format (*.gif) Portable Network Graphics (*.png) Windows Metafile (*.wmf) and Enhanced Metafile (*.emf) DICOM file format (*.dic, *.dcm, *.dicom, or files without file extension) Shortcut Ctrl+O Close File Close Closes the image window. 22

29 New Image from Clipboard File New image from Clipboard Creates a new image from a bitmap image on the clipboard. You place an image on the clipboard for example by using the Copy command on a graphics object in other software. Save File Save Allows to save the image in Digimizer native format (file extension.dgz), or in JPG, GIF, PNG or TIFF format. If you want to save the image as a new file, use the command Save as. Shortcut Ctrl+S Save as File Save as Select Save as to save the image as a new file on disk, or to save a file on a different disk. You will have to enter a new name for the image in the file selector box. Digimizer can save files in the following formats: Digimizer image format (*.dgz) (see also p. 3) JPEG Interchange format (*.jpg) (minimal compression) Tagged Image File Format (*.tif) Windows bitmap (*.bmp) Graphic Interchange Format (*.gif) Portable Network Graphics (*.png) 23

30 Select Scanner File Select Scanner Allows to select a TWAIN compliant scanner or camera - if available. TWAIN defines a standardized way to provide communication between imaging devices, such as a scanners or digital cameras, to software applications. Digimizer supports most TWAIN-compliant devices, but compatibility with particular scanning devices is not guaranteed. Acquire Image from Scanner File Acquire Image from Scanner Allows to acquire an image from a TWAIN compliant scanner or camera - if available. If you have several TWAIN devices, you select the TWAIN device using the Select Scanner command (see above), before acquiring the image. In your imaging software, do not select a color depth higher than 24-bits. MedCalc does not support 48- bit images (optionally produced by some scanners). Grab Image from Camera File Grab Image from Camera Allows to acquire an image from a life camera feed. In the dialog box you can select the camera and the image format. The different formats are displayed as compression, size and bitcount, e.g. RGB x 960 (24). Print File Print... Allows to print the contents of the image window. 24

31 Shortcut Ctrl+P Exit File Exit Stops the program. If the latest changes have not been saved, then the program will display an appropriate warning. In this case you will have the option to save the data (Yes), or exit the program without saving the data (No), or cancel the Exit command and stay in the program (Cancel). Shortcut Alt+F4 File - Measurements List menu New File Measurements List New Starts a new measurements list. Open File Measurements List Open Opens an existing Measurements List file. 25

32 Save File Measurements List Save Save the measurements list as a file. Save As File Measurements List Save As Saves the measurements list as a new file. Export File Measurements List Export Allows to export the measurements list as an Excel spreadsheet file, or as a MedCalc file for statistical analysis. 26

33 Edit menu Undo Edit Undo With the Undo command (if available) you can undo your most recent actions. Shortcut Ctrl+Z Cut Edit Cut Removes the selection from the window and places it on the Clipboard. The selection can then be pasted at another location. Shortcut Ctrl+X Copy Edit Copy Copies the selection from the window and places it on the Clipboard. The selection can then be pasted at another location. Shortcut Ctrl+C 27

34 Paste Edit Paste The Paste command is used to paste the contents of the clipboard onto the active window. Shortcut Ctrl+V Delete Edit Delete Deletes the current selection (does not affect the clipboard). Shortcut Del (Delete key) Duplicate Edit Duplicate Duplicates the current selection. Shortcut Ctrl+D 28

35 Select all Edit Select all Selects the entire contents of the active window. Shortcut Ctrl+A View menu Measurements List View Measurements List Opens or closes the measurements list window. The measurements list displays measurements in the current image, but can also include measurements of several images. 29

36 Statistics View Statistics Opens or closes the statistics window. The statistics window displays summary statistics (n, mean, SD, minimum and maximum) of the measurements in the Measurements list. Measurements List Columns View Measurements List Columns Allows to select the columns or measurements that are visible in the Measurements List and Statistics window. Dialog box Select the columns corresponding to the measurements of interest. 30

37 Click OK to proceed. Grid View Grid Allows to display or hide a grid in the image window. Zoom to Fit View Zoom Zoom to Fit Adjusts the zoom so that the image fits inside the window. 31

38 Shortcut Ctrl+0 Note This command does not change the physical size of the picture. Zoom In View Zoom In Allows to increase the zoom factor and show more detail. Shortcut Note Ctrl+ + Zooming in only magnifies the image on your screen; it does not change the physical size of the picture. Zoom Out View Zoom Out Allows to decrease the zoom factor and show less detail. Shortcut Note Ctrl+ - Zooming out only reduces the magnification of the image on your screen; it does not change the physical size of the picture. 32

39 Format menu Resize Format Resize Allows to resize the image. Dialog box Width and Height: select the required width or height. Option Lock aspect ratio: when this option is selected the ratio width:height will remain unchanged. Click OK to proceed. Crop Format Crop Cropping an image is removing unwanted border areas from an image. To crop the image, you: Select Crop in the Format menu Click a starting point in the image and drag the new outline After dragging the outline, you can make corrections to the outline rectangle Click OK in the Crop dialog box Dialog box 33

40 Width and Height: select the exact required width and height of the cropped image. Click OK to proceed. Example Before cropping: The new image outline is defined by dragging the mouse over the area of interest: After cropping: Rotate Format Rotate Rotate Clockwise Rotate Counterclockwise Allows to rotate the image clockwise or counterclockwise. 34

41 Example Before: Rotate clockwise: Rotate counterclockwise: Flip Format Flip Flip Horizontal Flip Vertical Allows to flip the image horizontally or vertically. Example Before: Flip horizontal: Flip vertical: Reset Calibration Format Reset Calibration Allows to reset the calibration. Note: this command is not available when a unit line is present in the image. To reset the calibration, you first remove the unit line, if present. select Reset Calibration in the menu. 35

42 If a default calibration is defined in the Options box (p. 62), then the calibration is reset to this default calibration. Image menu Contrast Auto Fix Image Contrast Auto Fix Maximizes contrast automatically. Example Before: After: Stretch Histogram Image Stretch Histogram Allows to optimize contrast by selecting a lower and upper threshold value. Dialog box The dialog box displays a histogram of gray levels. The upper and lower threshold values are represented by vertical red lines. 36

43 You drag the red lines to the required threshold values. pixels with a gray value less than the lower threshold value will be black. pixels with a gray value higher than the upper threshold value will be white. the gray values between the two threshold values will be stretched over the full range of possible gray values. Click Preview to judge the results. Click OK to proceed. Example Before: After: Background Correction Image Background Correction Corrects image defects caused by uneven illumination (e.g. in microscopy). 37

44 Example Before: After: Despeckle Image Despeckle Removes noise from images without blurring edges. Example Before: After: Convert to Grayscale Image Convert to Grayscale Converts the image to a grayscale image. 38

45 Example Before: After: Invert Image Invert Creates a negative of the image. Example Before: After: Negative Image Negative Allows to invert selected colors planes (red, green or blue). 39

46 Dialog box Select the color channels you want to invert. Click OK to proceed. Example Before: Invert Blue: Invert Red: Adjust colors Image Adjust colors Allows to increase or decrease the intensity of the red, green and blue color components in the image. Dialog box Use the sliders to increase or decrease the intensity of the 3 color components. 40

47 Click OK to proceed. Example Before: After: Selective color brightness Image Selective color brightness Allows to increase or decrease the brightness of red, green and blue pixels in the image. Dialog box Use the sliders to increase or decrease the brightness of red, green and blue pixels. E.g. if you move the slider for the red color to the right, then pixels with a high red component will appear lighter. Click OK to proceed. 41

48 Example Before: After: Sharpen Image Sharpen Applies a sharpen filter to the image. Dialog box Filter Size: larger filter yields stronger effect. Filter Intensity: % filter intensity. Click OK to proceed. Example Before: After: 42

49 Filters Canny Edge Detector Image Filters Canny Edge Detector Applies a Canny Edge Detector to an image. Dialog box Sigma: Standard deviation of the Gaussian filter. Good values to start with are between 0.6 and 2.4. Smaller filters cause less blurring, and allow detection of small, sharp lines. A larger filter increases processing time and causes more blurring. Low and High thresholds: A threshold set too high can miss important information. On the other hand, a threshold set too low will falsely identify irrelevant information (such as noise) as important are good starting values for the low threshold; are good starting values for the high threshold. Click Preview to judge the results. Click OK to proceed. Examples Before: After: 43

50 Emboss Filter Image Filters Emboss Filter Generates an embossed image. Dialog box Filter Size: controls depth of effect. Option Color emboss: preserves color in the image. Click Preview to judge the results. Click OK to proceed. Example Before: After: Arithmetic Mean Filter Image Filters Arithmetic Mean Filter Applies an arithmetic mean filter to an image. An arithmetic mean filter operation on an image removes short tailed noise such as uniform and Gaussian type noise from the image at the cost of blurring the image. The arithmetic mean filter is defined as the average of all pixels within a local region of an image. 44

51 The arithmetic mean is defined as: Pixels that are included in the averaging operation are specified by a mask. The larger the filtering mask becomes the more predominant the blurring becomes and less high spatial frequency detail that remains in the image. Dialog box Filter Size: size of the filter mask; a larger filter yields stronger effect. Click Preview to judge the results. Click OK to proceed. Examples Before: After: 45

52 Geometric Mean Filter Image Filters Geometric Mean Filter Applies a geometric mean filter to an image. In the geometric mean method, the color value of each pixel is replaced with the geometric mean of color values of the pixels in a surrounding region. A larger region (filter size) yields a stronger filter effect with the drawback of some blurring. The geometric mean is defined as: The geometric mean filter is better at removing Gaussian type noise and preserving edge features than the arithmetic mean filter. The geometric mean filter is very susceptible to negative outliers. Dialog box Filter Size: larger filter yields stronger effect. Click Preview to judge the results. Click OK to proceed. Examples Before: After: 46

53 Harmonic Mean Filter Image Filters Harmonic Mean Filter Applies a harmonic mean filter to an image. In the harmonic mean method, the color value of each pixel is replaced with the harmonic mean of color values of the pixels in a surrounding region. The harmonic mean is defined as: A larger region (filter size) yields a stronger filter effect with the drawback of some blurring. The harmonic mean filter is better at removing Gaussian type noise and preserving edge features than the arithmetic mean filter. The harmonic mean filter is very good at removing positive outliers. Dialog box Filter Size: larger filter yields stronger effect. Click Preview to judge the results. Click OK to proceed. 47

54 Examples Before: After: Median Filter Image Filters Median Filter Applies a median filter to an image. The median filter is defined as the median of all pixels within a local region of an image. The median filter is normally used to reduce noise in an image, somewhat like the mean filter. However, it often does a better job than the mean filter of preserving useful detail in the image. Dialog box 48

55 Filter Size: larger filter yields stronger effect. Click Preview to judge the results. Click OK to proceed. Examples Before: After: Maximum Filter Image Filters Maximum Filter Applies a maximum filter to an image. The maximum filter is defined as the maximum of all pixels within a local region of an image. The maximum filter is typically applied to an image to remove negative outlier noise. 49

56 Dialog box Filter Size: larger filter yields stronger effect. Click Preview to judge the results. Click OK to proceed. Examples Before: After: 50

57 Minimum Filter Image Filters Minimum Filter Applies a minimum filter to an image. The minimum filter is defined as the minimum of all pixels within a local region of an image. The minimum filter is typically applied to an image to remove positive outlier noise. Dialog box Filter Size: larger filter yields stronger effect. Click Preview to judge the results. Click OK to proceed. Examples Before: After: 51

58 Midpoint Filter Image Filters Midpoint Filter Applies a midpoint filter to an image. In the midpoint method, the color value of each pixel is replaced with the average of maximum and minimum (i.e. the midpoint) of color values of the pixels in a surrounding region. A larger region (filter size) yields a stronger effect. The midpoint filter is typically used to filter images containing short tailed noise such as Gaussian and uniform type noise. Dialog box Filter Size: larger filter yields stronger effect. Click Preview to judge the results. Click OK to proceed. Examples Before: After: 52

59 Range Filter Image Filters Range Applies a Range filter to an image. In the range method, the color value of each pixel is replaced with the difference of maximum and minimum (i.e. the range) of color values of the pixels in a surrounding region. The range filter is used to find edges within an image. Dialog box Filter Size: larger filter yields stronger effect. Click Preview to judge the results. Click OK to proceed. Examples Before: After: 53

60 Yp Mean Filter Image Filters Yp Mean Filter Applies a Yp Mean filter to an image. The Yp mean filter is member of a set of nonlinear mean filters which are better removing Gaussian type noise and preserving edge features than the arithmetic mean filter. Yp mean filter is very good at removing positive outliers for negative values of P and negative outliers for positive values of P (Power, see below). Dialog box Filter Size: larger filter yields stronger effect. Power: controls power. P<0 removes positive outliers; P>0 removes negative outliers. Click Preview to judge the results. Click OK to proceed. Examples Before: After: 54

61 Binary menu Binarization Binary Binarization Converts an image to a binary image by converting all pixels below a user-selected threshold value to red and those above to white. Dialog box The dialog box displays a histogram of gray levels. In the histogram you drag the red line to the required threshold value. 55

62 All gray levels below the threshold value will become red (indicating an object), those above white (indicating background). Click Preview to judge the results. Click OK to proceed. Example Before: After: Overlay Binary Image Binary Overlay Binary Image Option to show the Binary Image as a semi-transparent layer over the original image. Example Overlay binary image Off: Overlay binary image On: Hide Binary Layer Binary Hide Binary Layer Option to hide or show the binary image layer. 56

63 Morphological Dilate Binary Morphological Operations Dilate This filter will morphologically dilate the binary image. Binary dilation of an object increases its geometrical area by setting the background pixels adjacent to an object s contour to the object s gray level value. The filter adds pixels at region boundaries and fills in holes. Example Before: After: Morphological Erode Binary Morphological Operations Erode This filter will morphologically erode the binary image. Binary dilation of an object reduces its geometrical area by setting the contour pixels of an object to the background value. The filter removes pixels at boundaries or regions and increases the size of holes. Example Before: After: 57

64 Morphological Close Binary Morphological Operations Close This filter will morphologically close the binary image. Morphological closing of a binary image is defined as the dilation of the image followed by the erosion of the dilated image. The closing filter operation will smooth boundaries, reduce small inward bumps, join narrow breaks and fill small holes caused by noise. Example Before: After: Morphological Open Binary Morphological Operations Open This filter will morphologically open the binary image. Morphological opening of a binary image is defined as the erosion of that image followed by the dilation of the eroded image. The opening filter operation will smooth boundaries, reduce small outward bumps and small narrow openings within the object. Example Before: After: 58

65 Noise Reduction Binary Noise Reduction Reduces noise in the binary image. Example Before: After: Analyze Objects Binary Analyze Objects Allows to automatically extract object contours from the binary image. Dialog box 59

66 Minimum and maximum object dimensions: the minimum and/or maximum area or length of an object. Objects with smaller or larger area or length will be ignored. Option Exclude objects on image border: when this option is selected, objects that are on the border of the image will be ignored (since the object is not completely 'visible', area and perimeter of the object cannot be calculated accurately). Option Objects van contain other objects: select this option when objects are hollow and can contain other objects. Click OK to proceed. Example Before (binarized image): After: Import Binary Layer Binary Import Binary Layer from Image File Allows to import the binary layer from a different Digimizer image file (file extension.dgz). To fix the placement of the imported binary layer in the image use Set coordinates origin on matching points in both images. To fix possible magnification differences, use the Unit tool (p. 12) in both images. Tools menu Scripts Tools Scripts Allows to create and manage scripts. A script is a text with a sequence of commands. A different shortcut key can be assigned to each script. 60

67 Dialog box The left panel lists the available scripts. Buttons New: create a new script. Edit: edit the selected script. See Edit script. Delete: delete the selected script. Execute: execute the selected script. Edit script Allows to edit a script. Required input Script name: each script requires a unique name. Shortcut key: assign a shortcut key to the script. You can select a character in the range A..Z or For example, when you select the letter A, you will be able to execute the script by pressing the key combination Shift + Ctrl + A Script commands: a list of commands that make up the script. Script commands AnalyzeObjects [include exclude] [minarea maxarea] Extract object contours from the binary image. Optional parameters: include exclude: include or exclude objects that are on the image border minarea: minimum area of objects maxarea: maximum area of objects BackgroundCorrection Correct image defects caused by uneven illumination. Binarize [threshold] Convert the image to a binary image by converting all pixels below a threshold value to red and those above to white. Optional parameter: threshold: a value in the range [0..255] ContrastAutoFix Despeckle Maximize contrast automatically. Remove noise from images without blurring edges. Flip vertical horizontal Grayscale Invert Flip the image vertically or horizontally. Convert the image to a grayscale image. Create a negative of the image. Rotate left right MorphDilate MorphErode Rotate the image left or right. Add pixels at region boundaries and fill in holes (Morphological Dilate operation). 61

68 MorphOpen MorphClose SelectAll Remove pixels at boundaries or regions and increase the size of holes (Morphological Erode operation). Smooth boundaries, break narrow isthmuses and eliminate small noise regions (Morphological Open operation). Smooth boundaries, join narrow breaks and fill small holes caused by noise (Morphological Close operation). Selects all measurement objects in the image window. Sharpen [filtersize] [intensity] Apply a sharpen filter to the image. Optional parameters: filtersize: larger filter size yields stronger effect intensity: % filter intensity Options Tools Options Allows to configure the software and select different options. Dialog box Default calibration: select this option to use a default calibration. The default calibration is entered as number of pixels per unit of length. Digimizer offers the following units of length: kilometer (km), hectometer (hm), decameter (dam), meter (m), centimeter (cm), millimeter (mm), micrometer (µm), nanometer (nm), picometer (pm), femtometer (fm), attometer (am), inch (in), foot (ft), yard (yd), mile (mi), degrees ( ), units (u) (this is an unnamed relative unit), or pixels. Show result after finalizing measurement: when this option is selected, a small results window will be displayed after each measurement. Show circle quadrants: show quadrants in circle measurement objects. Show area centroid: show the centroid of objects in the image window. Do not ask to save unnamed measurements lists: when a measurement is added to the measurements list, the list is marked as 'changed', and you will be prompted to save the measurements list before clearing the list, or before you exit the program. If you don't need this reminder, select this option. Default zoom: enter an optional default zoom (1 to 2000). Invert image after scanning: option to invert the image after acquiring it from the scanner (see Acquire Image from Scanner, p. 24). Click OK to proceed. 62

69 Window menu Reset Window Layout Window Reset Window Layout Resets the Digimizer window layout to a default layout. Help menu Digimizer help Help Digimizer help Displays help. You select Digimizer help or press F1 to browse the comprehensive on-line documentation. In Help, click one of the following tabs: Click the Contents tab to browse through topics by category. Click the Index tab to see a list of index entries, and then either type a word or scroll through the list. Click the Find tab to search for words or phrases that may be contained in a Help topic. What's new? This help page lists the more important changes and new features in recent versions of Digimizer. The most recent additions and changes are listed at the top. 63

70 About Digimizer Help About Digimizer Displays program version and copyright notice. Dialog box This dialog box displays: the Digimizer version number copyright notice link to the Digimizer website Click OK to close. 64

71 Index About Digimizer Acquire image from scanner Adjust colors Analyze objects Angle tool Application window... 2 Area Area tool Arithmetic Mean Filter Average hue Background correction Binarization Binary image Analyze objects Binarization Hide Binary Layer Import Binary Layer Morphological Close Morphological Dilate Morphological Erode Morphological Open Noise reduction Overlay Binary Image Binary menu Brightness & Contrast controls Calibration Default calibration How to calibrate measurements... 4 Reset Unit tool Camera Canny Edge Detector Center tool Centroid Circle tool Close image Color selection tool Contrast Auto Fix Convert to grayscale Copy Count Crop Cut Delete Despeckle Duplicate Edit menu Edit script Emboss Filter Everage intensity Exit Filters Arithmetic Mean Filter Canny Edge Detector Emboss Filter Geometric Mean Filter Harmonic Mean Filter Maximum Filter Median Filter Midpoint Filter Minimum Filter Range Filter Yp Mean Filter Flip image Format menu Geometric center Geometric Mean Filter Grab image from camera Grid Harmonic Mean Filter Help Hide Binary Layer Image menu Import Binary Layer Installation... 1 Invert Length tool Live camera feed Load image file Lock tool Magic contour tool Marker/counter tool Maximum Filter Measurement tools Angle tool Area tool Center tool Circle tool Length tool Lock tool Magic contour tool Marker/counter tool Middle tool Path tool Perpendicular line tool Rectangle tool Select tool Unit tool Measurements List Columns Export New Open Save Save as View Measurements List menu Measurements toolbar Median Filter Middle tool Midpoint Filter Minimum Filter