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Digimizer

image analysis
software manual

MedCalc Software

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 purpose.
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 4.5

Digimizer

Copyright 2005-2015 MedCalc Software bvba


MedCalc Software
Acacialaan 22
8400 Ostend
Belgium
info@medcalc.org
www.medcalc.org
www.digimizer.com

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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iv

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
http://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 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 contain 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.

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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

When the Measurements list window is not visible, select the command View measurements list
(p. 29).

Click the

button

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

When the Statistics window is not visible, select the View statistics command (p. 30).

Click the

button

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.

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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 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.

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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:

- or -

Click on different objects while holding down the Ctrl key.

Drag a rectangle over the different objects.


To unselect objects:

- or

Click on the objects while holding down the Ctrl key.


Drag a rectangle over the objects while holding down the Ctrl key.

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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:

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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 cm 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 area
and 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 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.

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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 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.

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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 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

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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 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.

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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.

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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 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.

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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 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

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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.

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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

click in the image on the different objects

the number of objects is displayed in the Statistics window

or

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.

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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:

- or

enter a brightness value in the range -100 to 100 and press Enter,
use the up-down control to increase or decrease the brightness.

To change the image contrast:

- or

enter a contrast value in the range -100 to 100 and press Enter,
use the up-down control to increase or decrease the contrast.

Example
Before:

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Increased brightness:

Increased brightness
and contrast:

20

Related items
Contrast Auto Fix (p. 35)
Stretch Histogram (p. 36)

Zoom controls
Zoom factor
To change the zoom factor:

- or

enter the zoom factor in the range 1 to 2000 and press Enter,
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.

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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 in
other software.

Save
Command
File
Save
Description
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
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 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
Command
File
Acquire Image
Description
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 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 support
48-bit images (optionally produced by some scanners).

Print
Command
File
Print ...
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 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
Command
File
Measurements 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
File
Measurements List
Save As
Description
Saves the measurements list as a new file.

Export
Command
File
Measurements List
Export
Description
Allows to export the measurements list as an Excel spreadsheet file, or as a MedCalc file for statistical
analysis.

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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 be
pasted 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 pasted
at 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
Edit
Delete
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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28

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 include
measurements of several images.

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29

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 Statistics
window.
Dialog box
Select the columns corresponding to the measurements of interest.

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30

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
View
Zoom 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 the
picture.

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31

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
Format
Resize
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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32

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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33

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
Format
Flip
Flip Horizontal
Flip Vertical
Description
Allows to flip the image horizontally or vertically.

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34

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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35

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 are
represented 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 of
possible gray values.
Click Preview to judge the results.
Click OK to proceed.

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36

Example
Before:

After:

Background Correction
Command
Image
Background Correction
Description
Corrects image defects caused by uneven illumination (e.g. in microscopy).
Example
Before:

After:

Despeckle
Command
Image
Despeckle
Description
Removes noise from images without blurring edges.

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37

Example
Before:

After:

Convert to Grayscale
Command
Image
Convert to Grayscale
Description
Converts the image to a grayscale image.
Example
Before:

After:

Invert
Command
Image
Invert
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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39

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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40

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 will
appear 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
Image
Filters
Canny Edge Detector
Description
Applies a Canny Edge Detector to an image.

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42

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.
0.2-0.5 are good starting values for the low threshold; 0.6-0.9 are good starting values for the high
threshold.
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 is
defined 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 filtering
mask becomes the more predominant the blurring becomes and less high spatial frequency detail that
remains 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
Image
Filters
Geometric Mean Filter
Description
Applies a geometric mean filter to an image.

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45

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:

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46

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 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.
Examples
Before:

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47

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 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

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 pixels
within 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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49

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 within
a 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:

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51

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 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:

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52

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 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:

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53

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 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:

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54

Binary menu
Binarization
Command
Binary
Binarization
Description
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.
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
Binary
Overlay 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
Binary
Hide 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 its
geometrical area by setting the background pixels adjacent to an objects contour to the objects gray
level 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 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:

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57

Morphological Close
Command
Binary
Morphological Operations
Close
Description
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
Command
Binary
Morphological Operations
Open
Description
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:

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58

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 border
of the image will be ignored (since the object is not completely 'visible', area and perimeter of the object
cannot be calculated accurately).
Click OK to proceed.

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Example
Before (binarized image):

After:

Import Binary Layer


Command
Binary
Import 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 matching
points 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 each
script.
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 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
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 Erode
operation).
MorphOpen
Smooth boundaries, break narrow isthmuses and eliminate small noise regions (Morphological
Open operation).
MorphClose
Smooth boundaries, join narrow breaks and fill small holes caused by noise (Morphological
Close operation).
SelectAll
Selects all measurement objects in the image window.
Sharpen [filtersize] [intensity]

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61

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 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 (m), 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

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, 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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62

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 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.

About Digimizer
Command
Help
About Digimizer
Description
Displays program version and copyright notice.
Dialog box

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63

This dialog box displays:

the Digimizer version number

copyright notice

link to the Digimizer website


Click OK to close.

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64

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 ................................................. 16
Background correction .................................. 37
Binarization ................................................... 55
Binary image
Analyze objects ..................................... 59
Binarization ............................................ 55
Hide Binary Layer .................................. 56
Import Binary Layer ............................... 60
Morphological Close .............................. 58
Morphological Dilate .............................. 57
Morphological Erode .............................. 57
Morphological Open .............................. 58
Noise reduction...................................... 59
Overlay Binary Image ............................ 56
Binary menu ................................................. 55
Brightness & Contrast controls ..................... 20
Calibration
Default calibration .................................. 62
How to calibrate measurements .............. 4
Reset ..................................................... 35
Unit tool ................................................. 12
Canny Edge Detector ................................... 42
Center tool .................................................... 17
Centroid ........................................................ 16
Circle tool ...................................................... 17
Close image .................................................. 22
Color selection tool ....................................... 20
Contrast Auto Fix .......................................... 35
Convert to grayscale ..................................... 38
Copy ............................................................. 27
Count ............................................................ 19
Crop .............................................................. 33
Cut ................................................................ 27
Delete ........................................................... 28
Despeckle ..................................................... 37
Duplicate....................................................... 28
Edit menu ..................................................... 27
Edit script ...................................................... 61
Emboss Filter ................................................ 43
Everage intensity .......................................... 16
Exit................................................................ 25
Filters
Arithmetic Mean Filter ............................ 44
Canny Edge Detector ............................ 42
Emboss Filter......................................... 43
Geometric Mean Filter ........................... 45
Harmonic Mean Filter ............................ 47
Maximum Filter ...................................... 49

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Median Filter ......................................... 48


Midpoint Filter ....................................... 52
Minimum Filter ...................................... 50
Range Filter .......................................... 53
Yp Mean Filter....................................... 54
Flip image .................................................... 34
Format menu................................................ 32
Geometric center ......................................... 16
Geometric Mean Filter.................................. 45
Grid .............................................................. 31
Harmonic Mean Filter ................................... 47
Help.............................................................. 63
Hide Binary Layer ........................................ 56
Image menu ................................................. 35
Import Binary Layer ...................................... 60
Installation ...................................................... 1
Invert ............................................................ 38
Length tool ................................................... 13
Load image file............................................. 22
Lock tool....................................................... 12
Magic contour tool ........................................ 19
Marker/counter tool ...................................... 19
Maximum Filter ............................................ 49
Measurement tools
Angle tool .............................................. 14
Area tool ............................................... 16
Center tool ............................................ 17
Circle tool .............................................. 17
Length tool ............................................ 13
Lock tool ............................................... 12
Magic contour tool................................. 19
Marker/counter tool ............................... 19
Middle tool ............................................ 13
Path tool ................................................ 15
Perpendicular line tool .......................... 14
Rectangle tool ....................................... 18
Select tool ............................................. 12
Unit tool ................................................. 12
Measurements List
Columns ................................................ 30
Export ................................................... 26
New....................................................... 25
Open ..................................................... 25
Save ...................................................... 26
Save as ................................................. 26
View ...................................................... 29
Measurements List menu ............................. 25
Measurements toolbar ................................. 11
Median Filter ................................................ 48
Middle tool.................................................... 13
Midpoint Filter .............................................. 52
Minimum Filter ............................................. 50
Morphological Close .................................... 58
Morphological Dilate .................................... 57
Morphological Erode .................................... 57
Morphological Open ..................................... 58
Negative ....................................................... 39

65

Noise reduction ............................................. 59


Open image file............................................. 22
Options ......................................................... 62
Overlay Binary Image ................................... 56
Paste ............................................................ 28
Path tool ....................................................... 15
Print .............................................................. 24
Radius .................................................... 17, 18
Range Filter .................................................. 53
Rectangle tool ............................................... 18
Reset calibration ........................................... 35
Reset window layout ..................................... 62
Resize........................................................... 32
Rotate image ................................................ 34
Roundness ................................................... 16
Save image ................................................... 23
Save image as .............................................. 23
Scripts........................................................... 60
Select all ....................................................... 29

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Select source ............................................... 24


Select tool .................................................... 12
Selective color brightness ............................ 41
Sharpen ....................................................... 41
Statistics window.......................................... 30
Stretch histogram ......................................... 36
System requirements ..................................... 1
Toolbar ......................................................... 10
Tools menu .................................................. 60
Undo ............................................................ 27
Unit tool ........................................................ 12
View menu ................................................... 29
Whats new .................................................. 63
Window menu .............................................. 62
Yp Mean Filter.............................................. 54
Zoom controls .............................................. 21
Zoom in ........................................................ 31
Zoom out ...................................................... 32
Zoom to Fit ................................................... 31

66