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Digimizer Manual
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7/21/2019 Digimizer Manual
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Digimizer image analysis
software manual
MedCalc Software
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© MedCalc Software bvba. All rights reserved. No part of this package, neither the documentation northe 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 thedocumentation and specifically disclaim any implied warranties of fitness for any particular purpose.
Microsoft , Excel , Windows and Windows Vista are trademarks or registered trademarks of MicrosoftCorporation in the United States and/or other countries.
Digimizer and MedCalc are registered trademarks.
Version 4.5
Digimizer
Copyright 2005-2015 MedCalc Software bvba
MedCalc Software
Acacialaan 228400 OstendBelgium
www.medcalc.org
www.digimizer.com
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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 ................................................................................ .............................................................. .... 10 File controls ...................................................... ................................................................. ............ 10 Edit controls ................................................................ ................................................................ .. 10 Rotate & Flip controls - Crop control ............................................................................................. 10 Measurements toolbar ..................................................................... ............................................. 11
Measurements tools ...................................................................................................... ....................... 12
Select tool ............................................................................. ........................................................ 12 Lock tool ........................................................... ................................................................. ............ 12 Unit tool ............................................................................................ ............................................. 12 Length tool ................................................................. ............................................................... .... 13 Middle tool .............................................................................................................. ....................... 13 Angle tool ......................................................... ................................................................. ............ 14 Perpendicular line tool ............................................................ ....................................................... 14
Path tool ........................................................................................... ............................................. 15 Area tool ........................................................... ................................................................. ............ 16 Center tool..................................................................................................................................... 17 Circle tool .............................................................................. ........................................................ 17 Rectangle tool ....................................................................... ........................................................ 18 Marker/Counter tool ............................................................... ....................................................... 19 Magic contour tool ................................................................. ........................................................ 19 Color selection tool ................................................................ ........................................................ 20 Brightness & Contrast controls ......................................................... ............................................. 20 Zoom controls ....................................................................... ........................................................ 21
Menu overview .................................................................................................... .................................. 22
File menu .................................................................................... ........................................................ 22
Open Image ................................................................ ................................................................ .. 22
Close ..................................................... ................................................................. ....................... 22 New Image from Clipboard............................... ................................................................. ............ 23 Save ...................................................... ................................................................. ....................... 23 Save as ............................................................................................ ............................................. 23 Select Source ......................................................................................................... ....................... 24 Acquire Image ............................................................. ................................................................. . 24 Print ....................................................... ................................................................. ....................... 24 Exit ........................................................ ................................................................. ....................... 25
File - Measurements List menu .............................................................. ............................................. 25
New ....................................................... ................................................................. ....................... 25 Open ................................................................................................ ............................................. 25 Save ...................................................... ................................................................. ....................... 26 Save As .................................................................................................................. ....................... 26
Export ............................................................... ................................................................. ............ 26
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Edit menu .......................................................................................................... .................................. 27
Undo ............................................................................................................................................. 27 Cut ................................................................................................................................................ 27 Copy ...................................................... ................................................................. ....................... 27 Paste ..................................................... ................................................................. ....................... 28 Delete ............................................................... ................................................................. ............ 28 Duplicate ................................................................................................................ ....................... 28 Select all........................................................................................................................................ 29
View menu ....................................................................... ............................................................... .... 29
Measurements List .................................................................................................................... .... 29 Statistics ........................................................... ................................................................. ............ 30 Measurements List Columns ............................................................ ............................................. 30 Grid .................................................................................................. ............................................. 31 Zoom to Fit ....................................................... ................................................................. ............ 31 Zoom In ....................................................................................................... .................................. 31 Zoom Out ......................................................................................... ............................................. 32
Format menu ................................................................................................................ ....................... 32
Resize .................................................................................................................... ....................... 32 Crop ................................................................................................. ............................................. 33
Rotate ........................................................................................................................................... 34 Flip ......................................................................................... ....................................................... 34 Reset Calibration ......................................................... .............................................................. .... 35
Image menu ........................................................................................... ............................................. 35
Contrast Auto Fix .................................................................. ........................................................ 35 Stretch Histogram ............................................................................ ............................................. 36 Background Correction .................................................................... ............................................. 37 Despeckle ................................................................................................... .................................. 37 Convert to Grayscale .................................................. .............................................................. .... 38 Invert ..................................................... ................................................................. ....................... 38 Negative ........................................................... ................................................................. ............ 39 Adjust colors.................................................................................................................................. 40 Selective color brightness .......................................... ............................................................... .... 41 Sharpen ........................................................................................................................................ 41
Filters ..................................................................................................... ............................................. 42
Canny Edge Detector ............................................................. ....................................................... 42 Emboss Filter .............................................................................................. .................................. 43 Arithmetic Mean Filter .................................................................................................... ............... 44 Geometric Mean Filter ............................................................ ....................................................... 45 Harmonic Mean Filter ............................................................................................. ....................... 47 Median Filter ......................................................................... ........................................................ 48 Maximum Filter ............................................................ ................................................................. . 49 Minimum Filter ............................................................. ................................................................. . 50 Midpoint Filter .............................................................. ................................................................. . 52 Range Filter................................................................................................................................... 53 Yp Mean Filter ............................................................. ................................................................. . 54
Binary menu ................................................................................................................. ....................... 55
Binarization ...................................................................................... ............................................. 55 Overlay Binary Image ............................................................. ....................................................... 56 Hide Binary Layer ........................................................ .............................................................. .... 56 Morphological Dilate ....................................................................................................... ............... 57 Morphological Erode ........................................................................ ............................................. 57 Morphological Close .................................................................................................................. .... 58 Morphological Open ............................................................................................... ....................... 58 Noise Reduction .......................................................... ................................................................. . 59 Analyze Objects .......................................................... ................................................................. . 59 Import Binary Layer ................................................................ ....................................................... 60
Tools menu ...................................................................... ............................................................... .... 60
Scripts .................................................................................................................... ....................... 60 Edit script ................................................................... ............................................................... .... 61
Options ............................................................. ................................................................. ............ 62
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Window menu .................................................................. ............................................................... .... 62
Reset Window Layout ...................................................................... ............................................. 62
Help menu .............................................................. ................................................................. ............ 63
Digimizer help ............................................................. ................................................................. . 63 What's new? ..................................................... ................................................................. ............ 63 About Digimizer ........................................................... ................................................................. . 63
Index ......................................................................................................... ............................................. 65
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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 andabout 8 Megabyte free space on the hard disk.
Software installation
If you have downloaded the software from the Internet, you should locate the setup filedigimizersetup.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 Digimizerfirst.
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 inDigimizer 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 sitehttp://www.digimizer.com/download/.
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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 allmenu 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 isdisplayed in a small popup window. See p. 10 for a short description for all buttons on the toolbar.
Measurement tools
The measurement tools toolbar contain the different tools for manual measurements in the image. Foran overview of all measurements tools, see p. 11.
Measurements list
The measurements list contains the different measurements performed in one or more images.
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Only the parameters selected in the Measurements List Columns options box (p. 35) aredisplayed 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 MedCalcfile 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 inthe 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 formatdo not only contain the image in a compressed format (without quality loss), but also themeasurements performed in this image.
When you re-open such file the measurements are added –if not already there – to the currentmeasurements list, and you can add, delete or modify the measurements.
All measurements performed in Digimizer have a global unique identifier number. These identifiersprevent that re-opening the file results in duplicates in the measurements list.
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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 oneend 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.
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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.
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The dialog box displays a histogram of gray levels. A red line indicates the default thresholdvalue.
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 minimumarea of 3 cm² is required for an object to be identified as a leaf):
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The leafs are now outlined.
The characteristics of the 6 leafs are displayed in the measurements list, and the mean areaand perimeter are displayed in the statistics window:
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Select Hide Binary layer in the Binary menu so you can judge how well the areas fit the leafs.
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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. 34)
Flip vertically (p. 34)
Straighten image (p. 4)
Crop image (p. 33)
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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 ameasurement using any of the tools below. Close the lock when you need to performseveral 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 perpendicularon 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 andperimeter.
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.
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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 theleft 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 anyof 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.
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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 asmall 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 thestatus 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 asmall window next to the object.
Summary statistics for all lengths measured with the Length tool are displayed in the Statisticswindow.
* Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in theMeasurements 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
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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 aredisplayed 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 lengthare displayed in a small window next to the object.
Summary statistics for all total lengths measured with the Middle tool are displayed in the Statisticswindow.
* Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in theMeasurements 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 aredisplayed 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 asmall 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 theMeasurements 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 firstline. The middle point of the second line is shown.
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Tip: while you are moving the mouse to the second and third position, lengths and angles aredisplayed 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 angleare displayed in a small window next to the object.
Summary statistics for all lengths and angles measured with the Perpendicular line tool are displayedin the Statistics window.
* Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in theMeasurements 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 thestatus 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 displayedin 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 theMeasurements list window.
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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 youpress the Ctrl key whilst moving the mouse.
While you are moving the mouse to the next position, lengths and angles are displayed in thestatus bar at the bottom of the Digimizer window.
Measurements
The surface area, perimeter, length, width, centroid (geometric center) , roundness, average intensityand hue are displayed in the Measurements list window (*).
Roundness is defined by (4*PI*Area) / (Perimeter*Perimeter) and is a number between 0 and1. 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 anypoint 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 aredisplayed in a small window next to the object.
Summary statistics for all areas, perimeters, lengths, widths and average intensities measured with theArea tool are displayed in the Statistics window.
* Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in theMeasurements list window.
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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 Ctrlkey whilst moving the mouse.
While you are moving the mouse to the next position, lengths and angles are displayed in thestatus 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 asmall window next to the object.
Summary statistics for all radiuses measured with the Center tool are displayed in the Statisticswindow.
* Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in theMeasurements 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
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Tips
While you are moving the mouse to the center position, radius and angles are displayed in thestatus 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 Circletool are displayed in the Statistics window.
* Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in theMeasurements 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 listwindow (*).
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, widthand height are displayed in a small window next to the object.
Summary statistics for all areas, perimeters, widths, lengths, and average intensities measured with theRectangle tool are displayed in the Statistics window.
* Only the parameters selected in the Measurements List Columns options box (p. 30) are displayed in theMeasurements list window.
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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 listwindow (*).
When the option Show result after finalizing measurement is selected, then the area and perimeter aredisplayed in a small window next to the object.
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Summary statistics for all areas, perimeters, lengths, widths and average intensities measured with theMagic 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 theMeasurements 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 brightnessand contrast:
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Related items
Contrast Auto Fix (p. 35)
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 overthe area of interest.
Note
Zooming only magnifies the image on your screen; it does not change the physical size of the picture.
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Menu overview
File menu
Open Image
Command
File
Open Image
Description
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
Command
File
Close
Description
Closes the image window.
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New Image from Clipboard
Command
File
New image from Clipboard
Description
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 inother software.
Save
Command
FileSave
Description
Allows to save the image in Digimizer native format (file extension .dgz), or in JPG, GIF, PNG or TIFFformat.
If you want to save the image as a new file, use the command Save as .
Shortcut
Ctrl+S
Save as
Command
File
Save as
Description
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)
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Select Source
Command
File
Select Source
Description
Allows to select a TWAIN compliant scanner or camera - if available.
TWAIN defines a standardized way to provide communication between imaging devices, such as ascanners or digital cameras, to software applications. Digimizer supports most TWAIN-compliantdevices, but compatibility with particular scanning devices is not guaranteed.
Acquire Image
Command
File
Acquire Image
Description
Allows to acquire an image from a TWAIN compliant scanner or camera - if available. If you haveseveral TWAIN devices, you select the TWAIN device using the Select Source command (see above),before acquiring the image.
In your imaging software, do not select a color depth higher than 24-bits. MedCalc does not support48-bit images (optionally produced by some scanners).
Command
FilePrint ...
Description
Allows to print the contents of the image window.
Shortcut
Ctrl+P
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Exit
Command
File
Exit
Description
Stops the program.
If the latest changes have not been saved then the program will display an appropriate warning. In thiscase 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
Command
FileMeasurements List
New
Description
Starts a new measurements list.
Open
Command
File
Measurements List
Open
Description
Opens an existing Measurements List file.
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Save
Command
File
Measurements List
Save
Description
Save the measurements list as a file.
Save As
Command
FileMeasurements List
Save As
Description
Saves the measurements list as a new file.
Export
Command
FileMeasurements List
Export
Description
Allows to export the measurements list as an Excel spreadsheet file, or as a MedCalc file for statisticalanalysis.
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Edit menu
Undo
Command
Edit
Undo
Description
With the Undo command (if available) you can undo your most recent actions.
Shortcut
Ctrl+Z
Cut
Command
Edit
Cut
Description
Removes the selection from the window and places it on the Clipboard. The selection can then bepasted at another location.
Shortcut
Ctrl+X
Copy
Command
Edit
Copy
Description
Copies the selection from the window and places it on the Clipboard. The selection can then be pastedat another location.
Shortcut
Ctrl+C
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Paste
Command
Edit
Paste
Description
The Paste command is used to paste the contents of the clipboard onto the active window.
Shortcut
Ctrl+V
Delete
Command
EditDelete
Description
Deletes the current selection (does not affect the clipboard).
Shortcut
Del (Delete key)
Duplicate
Command
Edit
Duplicate
Description
Duplicates the current selection.
Shortcut
Ctrl+D
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Select all
Command
Edit
Select all
Description
Selects the entire contents of the active window.
Shortcut
Ctrl+A
View menu
Measurements List
Command
View
Measurements List
Description
Opens or closes the measurements list window.
The measurements list displays measurements in the current image, but can also includemeasurements of several images.
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Statistics
Command
View
Statistics
Description
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
Command
View
Measurements List Columns
Description
Allows to select the columns or measurements that are visible in the Measurements List and Statisticswindow.
Dialog box
Select the columns corresponding to the measurements of interest.
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Click OK to proceed.
Grid
Command
View
Grid
Description
Allows to display or hide a grid in the image window.
Zoom to Fit
Command
View
Zoom
Zoom to Fit
Description
Adjusts the zoom so that the image fits inside the window.
Shortcut
Ctrl+0
Note
This command does not change the physical size of the picture.
Zoom In
Command
ViewZoom In
Description
Allows to increase the zoom factor and show more detail.
Shortcut
Ctrl+ +
Note
Zooming in only magnifies the image on your screen; it does not change the physical size of thepicture.
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Zoom Out
Command
View
Zoom Out
Description
Allows to decrease the zoom factor and show less detail.
Shortcut
Ctrl+ -
Note
Zooming out only reduces the magnification of the image on your screen; it does not change the
physical size of the picture.
Format menu
Resize
FormatResize
Description
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.
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Crop
Command
Format
Crop
Description
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
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:
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After cropping:
Rotate
Command
Format
Rotate
Rotate Clockwise
Rotate Counterclockwise
Description
Allows to rotate the image clockwise or counterclockwise.
Example
Before: Rotate clockwise: Rotate counterclockwise:
Flip
Command
FormatFlip
Flip Horizontal
Flip Vertical
Description
Allows to flip the image horizontally or vertically.
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Example
Before: Flip horizontal: Flip vertical:
Reset Calibration
Command
Format
Reset Calibration
Description
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.
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
Command
Image
Contrast Auto Fix
Description
Maximizes contrast automatically.
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Example
Before: After:
Stretch Histogram
Command
Image
Stretch Histogram
Description
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 arerepresented by vertical red lines.
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 ofpossible gray values.
Click Preview to judge the results.
Click OK to proceed.
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Example
Before: After:
Background Correction
Command
Image
Background Correction
Description
Corrects image defects caused by uneven i llumination (e.g. in microscopy).
Example
Before: After:
Despeckle
Command
Image
Despeckle
Description
Removes noise from images without blurring edges.
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Example
Before: After:
Convert to Grayscale
Command
Image
Convert to Grayscale
Description
Converts the image to a grayscale image.
Example
Before: After:
Invert
Command
ImageInvert
Description
Creates a negative of the image.
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Example
Before: After:
Negative
Command
Image
Negative
Description
Allows to invert selected colors planes (red, green or blue).
Dialog box
Select the color channels you want to invert.
Click OK to proceed.
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Example
Before: Invert Blue: Invert Red:
Adjust colors
Command
Image
Adjust colors
Description
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.
Click OK to proceed.
Example
Before: After:
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Selective color brightness
Command
Image
Selective color brightness
Description
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 willappear lighter.
Click OK to proceed.
Example
Before: After:
Sharpen
Command
Image
Sharpen
Description
Applies a sharpen filter to the image.
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Dialog box
Filter Size: larger filter yields stronger effect.
Filter Intensity: % filter intensity.
Click OK to proceed.
Example
Before: After:
Filters
Canny Edge Detector
Command
ImageFilters
Canny Edge Detector
Description
Applies a Canny Edge Detector to an image.
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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 increasesprocessing time and causes more blurring.
Low and High thresholds: A threshold set too high can miss important information. On the otherhand, a threshold set too low will falsely identify irrelevant information (such as noise) as important.0.2-0.5 are good starting values for the low threshold; 0.6-0.9 are good starting values for the highthreshold.
Click Preview to judge the results.Click OK to proceed.
Examples
Before: After:
Emboss Filter
Command
Image
Filters
Emboss Filter
Description
Generates an embossed image.
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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
Command
Image
Filters
Arithmetic Mean Filter
Description
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 isdefined as the average of all pixels within a local region of an image.
The arithmetic mean is defined as:
Pixels that are included in the averaging operation are specified by a mask. The larger the filteringmask becomes the more predominant the blurring becomes and less high spatial frequency detail thatremains in the image.
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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:
Geometric Mean Filter
Command
ImageFilters
Geometric Mean Filter
Description
Applies a geometric mean filter to an image.
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In the geometric mean method, the color value of each pixel is replaced with the geometric mean ofcolor values of the pixels in a surrounding region. A larger region (filter size) yields a stronger filtereffect 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 thanthe 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:
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Harmonic Mean Filter
Command
Image
Filters
Harmonic Mean Filter
Description
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 ofcolor 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 thanthe 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.
Examples
Before: After:
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Median Filter
Command
Image
Filters
Median Filter
Description
Applies a median filter to an image. The median filter is defined as the median of all pixels within alocal 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
Filter Size: larger filter yields stronger effect.
Click Preview to judge the results.
Click OK to proceed.
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Examples
Before: After:
Maximum Filter
Command
Image
Filters
Maximum Filter
Description
Applies a maximum filter to an image. The maximum filter is defined as the maximum of all pixelswithin a local region of an image.
The maximum filter is typically applied to an image to remove negative outlier noise.
Dialog box
Filter Size: larger filter yields stronger effect.
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Click Preview to judge the results.
Click OK to proceed.
Examples
Before: After:
Minimum Filter
Command
Image
Filters
Minimum Filter
Description
Applies a minimum filter to an image. The minimum filter is defined as the minimum of all pixels withina local region of an image.
The minimum filter is typically applied to an image to remove positive outlier noise.
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Dialog box
Filter Size: larger filter yields stronger effect.
Click Preview to judge the results.
Click OK to proceed.
Examples
Before: After:
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Midpoint Filter
Command
Image
Filters
Midpoint Filter
Description
Applies a midpoint filter to an image.
In the midpoint method, the color value of each pixel is replaced with the average of maximum andminimum (i.e. the midpoint) of color values of the pixels in a surrounding region. A larger region (filtersize) yields a stronger effect.
The midpoint filter is typically used to filter images containing short tailed noise such as Gaussian anduniform type noise.
Dialog box
Filter Size: larger filter yields stronger effect.
Click Preview to judge the results.
Click OK to proceed.
Examples
Before: After:
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Range Filter
Command
Image
Filters
Range
Description
Applies a Range filter to an image.
In the range method, the color value of each pixel is replaced with the difference of maximum andminimum (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:
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Yp Mean Filter
Command
Image
Filters
Yp Mean Filter
Description
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 Gaussiantype noise and preserving edge features than the arithmetic mean filter. Yp mean filter is very good atremoving 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:
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Binary menu
Binarization
Command
Binary
Binarization
Description
Converts an image to a binary image by converting all pixels below a user-selected threshold value tored 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.
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.
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Example
Before: After:
Overlay Binary Image
Command
BinaryOverlay Binary Image
Description
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
Command
BinaryHide Binary Layer
Description
Option to hide or show the binary image layer.
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Morphological Dilate
Command
Binary
Morphological Operations
Dilate
Description
This filter will morphologically dilate the binary image. Binary dilation of an object increases itsgeometrical area by setting the background pixels adjacent to an object’s contour to the object’s graylevel value. The filter adds pixels at region boundaries and fills in holes.
Example
Before: After:
Morphological Erode
Command
Binary
Morphological Operations
Erode
Description
This filter will morphologically erode the binary image. Binary dilation of an object reduces itsgeometrical area by setting the contour pixels of an object to the background value. The filter removespixels at boundaries or regions and increases the size of holes.
Example
Before: After:
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Morphological Close
Command
Binary
Morphological Operations
Close
Description
This filter will morphologically close the binary image. Morphological closing of a binary image isdefined 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 andfill small holes caused by noise.
Example
Before: After:
Morphological Open
Command
Binary
Morphological Operations
Open
Description
This filter will morphologically open the binary image. Morphological opening of a binary image isdefined 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 narrowopenings within the object.
Example
Before: After:
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Noise Reduction
Command
Binary
Noise Reduction
Description
Reduces noise in the binary image.
Example
Before: After:
Analyze Objects
Command
Binary
Analyze Objects
Description
Allows to automatically extract object contours from the binary image.
Dialog box
Minimum object area: the minimum area of an object. Objects with a smaller area will be ignored.
Maximum object area: the maximum area of an object. Objects with a larger area will be ignored.
Option Exclude objects on image border : when this option is selected, objects that are on the borderof the image will be ignored (since the object is not completely 'visible', area and perimeter of the objectcannot be calculated accurately).
Click OK to proceed.
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Example
Before (binarized image): After:
Import Binary Layer
Command
BinaryImport Binary Layer from Image File
Description
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 matchingpoints in both images.
To fix possible magnification differences, use the Unit tool (p. 12) in both images.
Tools menu
Scripts
Command
Tools
Scripts
Description
Allows to create and manage scripts.
A script is a text with a sequence of commands. A different shortcut key can be assigned to eachscript.
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.
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Edit script
Description
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 1..9.For example when you select the letter A, you will be able to execute the script by pressing the keycombination 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 andthose above to white. Optional parameter:
threshold: a value in the range [0..255]
ContrastAutoFix
Maximize contrast automatically.
Despeckle
Remove noise from images without blurring edges.
Flip vertical | horizontal
Flip the image vertically or horizontally.
Grayscale
Convert the image to a grayscale image.
Invert
Create a negative of the image.
Rotate left | right
Rotate the image left or right.
MorphDilate Add pixels at region boundaries and fill in holes (Morphological Dilate operation).
MorphErode
Remove pixels at boundaries or regions and increase the size of holes (Morphological Erodeoperation).
MorphOpen
Smooth boundaries, break narrow isthmuses and eliminate small noise regions (MorphologicalOpen operation).
MorphClose
Smooth boundaries, join narrow breaks and fill small holes caused by noise (MorphologicalClose operation).
SelectAll
Selects all measurement objects in the image window.
Sharpen [filtersize] [intensity]
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Apply a sharpen filter to the image.
Optional parameters:
filtersize: larger filter size yields stronger effect
intensity: % filter intensity
Options
Command
Tools
Options
Description
Allows to configure the software and select different options.
Dialog box
Default calibration: select this option to use a default calibration. The default calibration isentered 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 resultswindow will be displayed after each measurement.
Show circle quadrants: show quadrants in circle measurement objects
Do not ask to save unnamed measurements lists: when a measurement is added to themeasurements list, the list is marked as 'changed', and you will be prompted to save themeasurements list before clearing the list, or before you exit the program. If you don't need thisreminder, 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, p. 24).
Click OK to proceed.
Window menu
Reset Window Layout
Command
Window
Reset Window Layout
Description
Resets the Digimizer window layout to a default layout.
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Help menu
Digimizer help
Command
Help
Digimizer help
Description
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 thelist.
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. Themost recent additions and changes are listed at the top.
About Digimizer
Command
Help
About Digimizer
Description
Displays program version and copyright notice.
Dialog box
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Index
About Digimizer ............................................ 63 Acquire image ............................................... 24 Adjust colors ................................................. 40 Analyze objects............................................. 59 Angle tool ...................................................... 14 Application window ......................................... 2 Area ..................................................... ......... 16 Area tool ....................................................... 16 Arithmetic Mean Filter ................................... 44 Average hue ................................................. 16Background correction .................................. 37
Binarization ................................................... 55Binary image Analyze objects ..................................... 59Binarization ............................................ 55Hide Binary Layer .................................. 56Import Binary Layer ............................... 60Morphological Close .............................. 58Morphological Dilate .............................. 57Morphological Erode .............................. 57Morphological Open .............................. 58Noise reduction ...................................... 59Overlay Binary Image ............................ 56
Binary menu ................................................. 55Brightness & Contrast controls ..................... 20Calibration
Default calibration .................................. 62How to calibrate measurements .............. 4Reset ..................................................... 35Unit tool ................................................. 12
Canny Edge Detector ................................... 42Center tool .................................................... 17Centroid ........................................................ 16Circle tool ...................................................... 17Close image .................................................. 22Color selection tool ....................................... 20Contrast Auto Fix .......................................... 35Convert to grayscale ..................................... 38Copy .................................................... ......... 27Count ............................................................ 19
Crop .............................................................. 33Cut ................................................................ 27Delete ....................................... .................... 28Despeckle ..................................................... 37Duplicate ....................................................... 28Edit menu ..................................................... 27Edit script ...................................................... 61Emboss Filter ................................................ 43Everage intensity .......................................... 16Exit ................................................................ 25Filters
Arithmetic Mean Filter ............................ 44Canny Edge Detector ............................ 42Emboss Filter ......................................... 43
Geometric Mean Filter ........................... 45Harmonic Mean Filter ............................ 47Maximum Filter .................. .................... 49
Median Filter ......................................... 48Midpoint Filter ....................................... 52Minimum Filter ...................................... 50Range Filter .......................................... 53Yp Mean Filter....................................... 54
Flip image .................................................... 34Format menu ................................................ 32Geometric center ......................................... 16Geometric Mean Filter.................................. 45Grid .............................................................. 31Harmonic Mean Filter ................................... 47
Help.............................................................. 63Hide Binary Layer ........................................ 56Image menu ................................................. 35Import Binary Layer ...................................... 60Installation ...................................................... 1Invert ............................................................ 38Length tool ................................................... 13Load image file ............................................. 22Lock tool....................................................... 12Magic contour tool ........................................ 19Marker/counter tool ...................................... 19Maximum Filter ............................................ 49Measurement tools
Angle tool .............................................. 14 Area tool ............................................... 16
Center tool ............................................ 17Circle tool .............................................. 17Length tool ............................................ 13Lock tool ............................................... 12Magic contour tool................................. 19Marker/counter tool ............................... 19Middle tool ............................................ 13Path tool ................................................ 15Perpendicular line tool .......................... 14Rectangle tool ....................................... 18Select tool ............................................. 12Unit tool ................................................. 12
Measurements ListColumns ................................................ 30
Export ................................................... 26New ..................................................... .. 25Open ..................................................... 25Save ...................................................... 26Save as ................................................. 26View ...................................................... 29
Measurements List menu ............................. 25Measurements toolbar ................................. 11Median Filter ................................................ 48Middle tool .................................................... 13Midpoint Filter .............................................. 52Minimum Filter ............................................. 50Morphological Close .................................... 58Morphological Dilate .................................... 57
Morphological Erode .................................... 57Morphological Open ..................................... 58Negative ..................................................... .. 39
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Noise reduction ............................................. 59Open image file............................................. 22Options ................................................ ......... 62Overlay Binary Image ................................... 56Paste ................................ ............................ 28Path tool ....................................................... 15Print .......................................... .................... 24
Radius ................................................. ... 17, 18Range Filter .................................................. 53Rectangle tool ............................................... 18Reset calibration ........................................... 35Reset window layout ..................................... 62Resize ........................................................... 32Rotate image ......... ....................................... 34Roundness ....................... ............................ 16Save image ................................................... 23Save image as .............................................. 23Scripts ........................................................... 60Select all ....................................................... 29
Select source ............................................... 24Select tool .................................................... 12Selective color brightness ............................ 41Sharpen ....................................................... 41Statistics window .......................................... 30Stretch histogram ......................................... 36System requirements ..................................... 1
Toolbar ....................................................... .. 10Tools menu .................................................. 60Undo ............................................................ 27Unit tool ...................................................... .. 12View menu ................................................... 29What’s new .................................................. 63Window menu .............................................. 62Yp Mean Filter .............................................. 54Zoom controls .............................................. 21Zoom in ........................................................ 31Zoom out ...................................................... 32Zoom to Fit ................................................... 31