ement

a su r
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Phase
MICROVISION Instruments
CE 1750 - Petite Montagne Sud
8, rue du Forez - 91047 Evry - France
Tél : (33) (0) 1 69 11 15 50
Fax : (33) (0) 1 69 11 15 51
Courriel : info@microvision.fr
 6th edition
S.A.S. au capital de 135 000 euros
 Areas 7.0
R.C.S. Corbeil - Essonnes : B 388 570 046
 octobre 2008
 Table of contents

1. Overview of Areas 5
Starting up Areas 5
The Areas work sheet 5
The menus 6
The tabs, pages and documents 7
The status bar 8
The structure of a work session 9
Preparing the equipment 9
Preparing the study 9
The sample analysis 9
Using the results 9
Protecting the settings 9
2. Preparing the equipment 11
List of video sources 11
Acquisition of the image 11
Controlling the microscope 12
The image processor 12
Calibration of the device 13
Pre-defined calibrations 14
Definition of a new calibration 14

3. Preparing the study 17

Defining the study 17
Detection method 18
Measurement area 18
Phase detection settings 18
Setting fixed thresholding 19
Setting color thresholding 20
Setting adaptative thresholding 20
Setting smoothing 21
Defining a macro 21
Object separation 22
Application of geometric criteria 23
Saving the study 23
Saved templates and files 23
4. Analysis of the sample 25
Sample analysis with a simple video source 25
Plotting a permanent test pattern 25
Taking measurements 25
Sample analysis with a source equipped with an indexed stage 26
Plotting a reference area 26
Taking measurements 26
Sample analysis with a video source equipped with a motorized stage 26
Defining the scan 27

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 Previewing the sample 27
Taking measurements 28
5. Overview of sample 29
Exports 30
6. Measurements table 31
Object sorting 33
Exports 33
7. Statistics and Graphs 35
Exports 37
8. Page layout and Report print-out 39
9. Secure operating modes 41

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 1. Overview of Areas

Areas is a software application for automatic measurement of the phases in a sample. The
results of the measurements are summarized in a table in the form of surfaces expressed in
real units or as a percentage of a reference surface.
Areas also measures all the objects making up the phases. The results are then presented with full
details, or grouped by area of interest, or summarized by statistical values.
Everything is done so that the user can use the results provided by Areas as smoothly as possible: a
work session can be saved and resumed later. The results can be exported to common calculation
applications, either in compatible files or simply by using Copy / Paste. Finally, images and results
are edited on a printer.

Starting up Areas
The Areas shortcut is normally accessible in the "Microvision Instruments" program group, located
in the "Programs" menu within the Windows "Start" menu.

The Areas work sheet

The work sheet is the window displayed when Areas starts up. It contains the standard elements of
the Windows environment: the title bar (1) which includes the system menu box (on the left), and
the window enlargement / reduction boxes (on the right), the menu bar (2) provides access to all of
the software's functions. When the sheet does not occupy the entire screen, it can be moved (by
clicking on the title bar) or resized (by clicking within the frame).
The toolbar (3) contains some buttons for quickly accessing the software's most used functions.
On the left of the sheet, some tabs (4) allow you to display either the video image or various docu-
ments that are representative of the work in hand: a history of the measured fields, the measure-
ments tables and statistics tables, the printed report.
The video image or the document occupies most of the sheet (5). They are bordered by rulers (6),
graduated in real units, and by scroll bars that are active when the document or the image is larger
than the window itself.
In the lower part of the work sheet, the status bar (8) contains information relating to the work in
progress.

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 1

The Areas work sheet

The menus
They provide access to all Areas functions. Here is a quick overview of them:
• the “File” menu is dedicated to the studies: start of a study and definition of its main properties;
saving the study, exporting and printing the results. It also enables you to archive, load and print
images.
• the “Edit” menu provides classic «copy/paste» functions that allow you to exchange images or
documents between different softwares. You can also cancel an action and access the image
annotation module.
• The “Image” menu is dedicated to the acquisition and management of video images: acquisi-
tion, storage and improvement of images.
• The “Measure” menu contains the functions used during a study: system calibration, properties
of the study, choice of phases and measurement tools.
• The “Results” menu manages the various documents shown on the “Table”, “Results” and “Re-
port” pages. It also provides access to dialog boxes for defining the contents of these documents
and items allowing you to display certain of them in windows that remain visible at all times.
• the “Layout” menu contains various more general options: customization of the environment and
measurement display options.
• the "?" menu: information about the Areas software, and secure operating modes.

The toolbar
The toolbar provides quick access to certain frequently used functions:

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 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

The Areas toolbar

1. Choice of the active video source

2. Live video image from the camera, or, acquisition of an image from a scanner.
3. Adjustment of the acquisition from a camera or improvement of the contrast of a captured im-
age.
4. Control motorized features of the microscope.
5. Freezing the video image.
6. Activation / Deactivation of position tracking, when the active video source is equipped with an
indexed or motorized displacement stage.
7. Name of the measurement being taken. This is a pop-up menu: clicking on it displays the list of
the defined phases and allows you to change the phase.
8. Adjusting automatic detection of the current phase.
9. Defines the field currently visible on the screen as the origin for an automatic scan (if the video
source is equipped with a motorized stage).
10 and 12. Switching from field to field:
With a motorized stage, the buttons are active and pilot the stage.
With an indexed displacement stage, the buttons are inactive: the field is changed by moving the
stage manually.
With a manual system, the field movement buttons are active and allow you to display the
measurements already taken.
11. Automatic phase detection
13. Analysis of the sample (motorized sources).
14. Selection tools
15. Manual plotting tools. The tools available depend on the type of phase selected.
16 Table properties: keys and measurements displayed in the tables, display formats.
17 Statistics properties.
18. Graph properties: measurement represented and curve parameters.
19. Report properties: documents displayed and page layout.
20. Display / Masking of the various documents created by Areas. Depending on the page currently
displayed on the screen, the document is displayed on the page, in a separate palette or in the
printed report.

The tabs, pages and documents

The tabs located on the left of the window allow you to display five pages representative of the cur-
rent study:
• The real-time video image is of course the most important page as it allows you to observe the
sample and to take the measurements.

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 The video image and the possibly superimposed profiles can be saved or printed using the cor-
responding options in the “File” menu. A part of the image can be selected and then transferred
to another software, using the “Copy” option in the “Edit” menu.
• The “Scanning” page presents either a background history or a mapping of the fields measured:
it represents the phases detected, superposed on the image that is under the camera while the
measurement is being taken.
The overview can also be displayed in a separate window and included in the printed report. A
part of the overview may be selected, copied and then transferred to another software.
• The “Table” page presents the complete list of the objects detected and the corresponding
measured values. The objects are sorted by phase or by measurement areas and can also be
grouped together.
• The “Results” page allows you to display four separate documents:
- the surfaces table, in which each field is represented by a line
- a table of statistical values calculated for the individual object measurements.
- a distribution histogram of one of these measurements
- the values represented in this histogram.
These documents can be displayed in a separate window that is included in the report, or copied
to external software.
• The “Report” is a true copy of the document that is likely to be printed. It always follows the
progress of the work in hand.
The report page layout can be personalized: size and contents of the header and footer, title and
order of the printed documents.

The status bar

The status bar is located at the very bottom of the sheet. It contains information relating to the work
in progress:

1 2 3 4 5 6 7 8

The Areas status bar

1. System date.
2. System time.
3. Scale in which the video image or the overview is displayed.
4. Name of the currently applied calibration.
5. Name of the image file, if loaded.
6. Reference of the sample being analyzed (or name of the “study” file in which the measurements
are saved)
7. Position of the crosshairs when you click on one of the graduated rulers. When you use the fram-
ing tool, the size of the selected area is displayed here.
8. Indicator of memory used on the computer.

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The structure of a work session

Preparing the equipment

During this stage, you essentially set:
• Video image acquisition and framing: using the options in the “Image” menu, you try to obtain a
sufficiently contrasted image on the screen.
• the calibration of the system; this operation consists in establishing the equivalence between a
real distance and the length that is visible on the screen.
The preparation of the equipment is presented in Chapter 2.

Preparing the study

Preparing the study consists in providing the software with the number and the names of the phases
to be measured as well as some of the characteristics of the sample to be analyzed.
Then, the "detection" of each phase is set, i.e. all of the image processes that will lead the
equipment to detect the phase in the video image. The programmed treatments are summarized in
a palette that can be displayed via the "Measure" menu.
These operations are described in Chapter 3.

The sample analysis

The analysis consists in bringing up different fields onto the screen one after the other to measure
them and possibly manually retouch the detected surfaces. The functions used are described in
Chapter 4.
Chapter 5 presents the “Scan” page which displays either the mapping of the sample or the back-
ground history of the measurements taken.

Using the results

This final stage consists in defining the presentation of the tables provided as well as the page layout
for the measurement report.
These functions are described in Chapters 6 to 8.

Protecting the settings

The settings made during the first two stages are fundamental and determine the validity of the
measurement results. It is possible to prevent these settings from being modified by setting the soft-
ware to a secure operating mode.
The secure operating modes are described in Chapter 9.

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 2. Preparing the equipment

List of video sources

The “Sources” sub-menu in the “Image” menu lists the installed hardware configurations. Each con-
figuration consists of a camera, an optical device (compound microscope, magnifying glass or ma-
crolens), certain elements of which may be motorized: The configuration(s) were defined using the
Nazca configuration software, which is also used to define the hardware settings and the various ca-
librations required.
The configuration(s) are defined using the Nazca configuration software, which is also used to define
the hardware settings and the various calibrations required.
Areas can work with all of the proposed sources, but only those equipped with an indexed or moto-
rized stage can be used to analyze areas larger than the camera’s field. Choose the appropriate con-
figuration.
The list of sources also has two options for working with files rather than real sources:
• “Read image files” allows you to successively analyze several images saved in tiff, bitmap or
jpeg format. Navigation is then done either via the “Next scene” and “Previous scene” items in
the “Images” menu or via the “Next field” and “Previous field” items in the “Measures” menu.
• “Read a mapping” allows you to analyze a preview or an overview saved in the Microvision Car-
tography format. The “Scanning” page then displays an overview of the sample as a watermark.
A mapping is analyzed in exactly the same way as a sample observed using a source equipped
with a motorized stage.

Acquisition of the image

The main functions associated with image acquisition available in the “Image” menu are:
• “Acquire continuously” allows you to display the image of the sample on the screen, if the cam-
era allows this.
This toolbar button is equivalent to the “Acquire continuously” item.

• “Set camera…” displays a dialog box that allows you to adjust the camera parameters. Although
this dialog box is specific to each camera, it always contains certain routine parameters: expo-
sure time, white balance, etc.

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 When the image is continuously acquired, this button is equivalent to the “Adjust acquisi-
tion” item. The standard setting is applied to the image if the <Caps> key on the key-
board is held down. Finally, if the image is frozen, this button displays a dialog box in
which you can adjust the image contrast and brightness.
• “Freeze image” stops the continuous acquisition; this may improve visual comfort.
This toolbar button is equivalent to the “Freeze image” item.

Controlling the microscope

This button on the toolbar, or the “Adjust microscope…” in the “Image” menu, displays a
dialog box that allows you to control motorized features of the microscope : filter wheel, lens
turret, diaphragm, etc.

The elements shown in black are the controllable elements of the microscope : they have been defi-
ned using the Nazca configuration software.
The filter wheel, the lens turret and the diaphragm are controlled by clicking on the arrows located
on the left and on the right of the position indicated.
X position, Y position and focus position are changed either with the arrow keys, or by defining a
precise value : click in the position, enter the value with the keyboard, and select by pressing the
<Enter> or <Return> key.

The image processor

When the active source contains a digital camera, certain processes can be applied to the conti-
nuously acquired and displayed images. They are defined with the “Set processor” item in the
“Image” menu, which opens the following dialog box:

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The first process proposed converts the camera image into black and white.
Background correction is a particularly interesting process when you perform a motorized scanning
using a microscope with light background lighting. It allows you to get rid of any lighting disparities.
In order to implement it:
• At the start of the study, move the stage to an area with no objects
• Click on the “Acquire background” button
• Bring the stage back to an area to be analyzed: the objects to be measured must be visible, as
the background is now uniform in color over the entire image. The “Apply correction” button
can be used to estimate the correction quality.
Background image acquisition must be performed each time the source is started, therefore ge-
nerally each time the software is started.

Background image, to be ac- One of the continuously acqui- The same image, with correc-
quired at the start of the study red images, without correction: tion: the background is uni-
the objects are visible, but the form, facilitating object detec-
background is not uniform tion

The “mirrors” functions apply symmetries to the image, or a 180° rotation when both are activated.
They can be used without restriction with non-motorized sources. When the source is equipped with
a motorized or indexed stage, the choice should be made once and for all in the Nazca configuration
software before performing the alignment adjustment.

Calibration of the device

Calibration consists of determining an equivalency between a real length and the apparent length on
the screen. A correct calibration is essential for Areas to run smoothly.

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Pre-defined calibrations
The “Calibration” sub-menu in the “Measure” menu provides a list of scales corresponding to the
various magnifications produced by the optical system: compound microscope objectives or the
lens’ zoom position.
These scales were defined using the Nazca configuration software. You therefore just have to select
the desired magnification for the system to be calibrated. This can be checked by placing a ruler or
a micrometer under the camera and checking that its graduations correspond to those on the Areas
rulers.

Definition of a new calibration

If the optical system does not have a fixed position (continuous zoom, for example), the “Calibra-
tion” sub-menu displays the “Define...” item which provides access to a special setup window,
shown below:

The list of the pre-defined distance scales (1) is displayed on the top left of this sheet. It also incor-
porates some buttons and a text box (2) for creating, modifying and deleting the scales. Each scale
is expressed in a measurement unit (3) which can be modified: conversion is automatic.
Two vertical reticules and two horizontal reticules are drawn on the screen. Proceed as follows:
• Place a ruler or a micrometer horizontally under the camera,
• Align two reticules with known graduations that are as far as possible from each other,
• Enter the indicated distance, expressed in the current unit, into the “X” text field (4).
The ratio between the distance entered and the number of points separating the two reticules defines

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the horizontal calibration factor, which is expressed as a current unit per pixel.
In principle, this factor is identical for the vertical reticle, but it can be checked as follows:
• Place the ruler or the micrometer vertically,
• Align the two reticules,
• Enter the indicated distance into the “Y” text field (4).
This defines the calibration factor for the vertical reticle and the “Y / X” ratio which must remain
close to 1. This ratio essentially depends on the precision with which the camera respects the video
standard. It is therefore not essential to always calibrate the system in both directions. If only one
direction is calibrated, the “Y / X” ratio, once defined, is used to calibrate the other direction.

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 3. Preparing the study

Defining the study

During this first stage, the user defines the phases that he wishes to analyse and documents the stu-
dy that is starting (reference of the sample, name of the operator, comment(s)). This is done using
the “New study...” item in the “File” menu.

The name of each phase is indicated in the left column. It can be modified once it has been partially
or totally selected. The two colored boxes are used to define the color and pattern used to plot the
detected phases.
The “Follow pre-defined scan” box is available at the bottom of the window if the video source is
equipped with a motorized stage. This type of scan automatically analyses all or part of a sample,
alternating image acquisition and movement of the sample.

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The “keep measured images” box allows you to associate the image of the fields with the measure-
ments taken. These images are especially displayed in the overview. They are integrated into the
study file.

Detection method
Most of the time, we try to detect the phases using appropriate image processes, described later in
this chapter. This method is “automatic”. This is mentioned in the right-hand column of the list of
phases.
However, sometimes this type of detection is imperfect or we may simply prefer to plot the outline
of the phase using the mouse. The pop-up menu to the right of the list thus offers two other detec-
tion methods in addition to “Automatic detection”:
- “Manual plotting”: no automatic detection will be performed; only the profiles drawn with the
mouse will be measured.
- “Permanent test pattern”: this is a specific case of manual plotting, which is reproduced identically
in all measured fields (it is generally a geometrical shape).

Measurement area
The phases are detected in the area seen by the camera sensor, which we call “video field”. This is
mentioned in the middle column of the list; it allows you to perform the most common analyses.
The “Measurement area” pop-up menu also allows you to indicate that a phase is included in ano-
ther one, which becomes its reference area This has several consequences:
- Only the objects contained in the reference area are taken into account during the analysis
- The measurement table can count and group together the objects contained in each object in its
reference area,
- the phase percentages are expressed in relation to the reference area.
It is thus possible to hierarchically organize the various phases to be measured. The only restriction
is that the phases used as references must be detected before those that they contain.
The same pop-up menu offers an additional option that is only useful if the video source is equipped
with an indexed or motorized stage: when the “Sample” option is selected, the operator can graphi-
cally define an area of any shape, larger than the field. Only the phases within this shape will be de-
tected and measured.

Phase detection settings

Before carrying out phase measurements, the detection to be performed must be set for each of the
defined phases.
Press this button in the tool bar (or use the “Phase detection” item in the “Measure” menu). A
palette appears summarising the four detection stages for each of the phases:

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• Thresholding, which extracts the phase to be measured from the
image. There are two methods:
“Fixed” thresholding consists in manually setting the values of
shades characterizing the objects. This method allows greater
detection precision but requires stable lighting and uniform
sample preparation. There are two versions which take into ac-
count either the levels of gray in the image or the three color
components: hue, saturation and intensity.
“Adaptive” thresholding enables detection of objects in fields
where the lighting is not uniform. It is always carried out on an
image converted into gray levels. The detection takes a few
seconds.
• Filtering, which corrects imperfect thresholding that leaves arte-
facts or does not fully detect objects. Filtering can be either a
simple "smoothing" of the outlines of the detected objects or a
macroinstruction comprising a succession of image processing
operations.
• possibly a separation of the detected objects in order to then….
• ... apply a criterion to the measured objects (this stage is also
optional).

Setting fixed thresholding

It is set in the following dialog box:

Setting threshold levels for a monochrome image

This window presents the histogram of the gray levels present in the image. During analysis of the
video field, the points in the image that are detected are those whose light intensity is within the
range represented by the colored bar.
You can first choose the shade range to be detected from the pop-up menu. You can then set the
thresholds defining thresholding. The result of the thresholding operation appears if you click on the
"Phase" button (superimposition of a mask on the thresholded parts of the image) or on the "Outli-
nes" button (the thresholded parts are bordered).
If the detection is not satisfactory, modify the threshold(s) by clicking on the setting bar until the bar
is in the desired position.

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Setting color thresholding
It is set in the following dialog box:

Setting threshold levels for a color image

This window presents three superimposed histograms and the associated thresholds :
• A color histogram of the shades present in the image; two thresholds define the rainbow shades
to be detected.
• a histogram (gray) of saturations; two thresholds determine whether the required colors are
rather dull (on the left) or sharp (on the right).
• a histogram (black) of intensities; two thresholds determine whether the required colors are
rather dark (on the left) or bright (on the right)
The points in the image which will be detected are those with each of their hue, saturation and in-
tensity components inside the defined range. To extract an initial color :
Click on one of these buttons and select the shade to be extracted in the video image.
Areas then calculates the color components of the image points in the designated area and
then, regulated by the defined tolerance, the lower and upper detection thresholds.
The result of the thresholding operation appears if you click on the "Phase" button (superimposition
of a mask on the thresholded parts of the image) or on the "Outlines" button (the thresholded parts
are bordered).
If the detection carried out is not satisfactory, there are several ways of adjusting it:
• if the particles are incomplete, increase the tolerance; if too many objects were detected, de-
crease the tolerance.
• if the required objects are of sharp color, click in the value located on the right of the second
scale: this defines the high threshold of saturation in its maximum value.
• if the required objects are bright, click in the value located on the right of the third scale: this
defines the high threshold of the intensity in its maximum value. If they are dark, click in the
value located on the left of the bar.

Setting adaptative thresholding

This method is set with the following dialog box:

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 Setting adaptative thresholding

Here you will indicate:

• The general shade of the objects,
• A size parameter which relates to the radius of the largest objects to be detected,
• The minimum shading variation to take into account between the objects and the image back-
ground.
As in the previous case, the result of the thresholding operation will appear if you click on the
“Phase” button (the thresholded parts are colored) or on the “Outlines” button (the thresholded
parts are bordered).

Setting smoothing
The smoothing dialog box is presented as follows:

Setting smoothing

If small insignificant objects interfere with the measurement: increase the smoothing. If various ele-
ments of a phase are assimilated, reduce the smoothing.
The result of the thresholding operation appears if you click on the "Phase" button (superimposition
of a mask on the thresholded parts of the image) or on the "Outlines" button (the thresholded parts
are bordered).

Defining a macro
A “macro” is a series of cleverly arranged image transformations: it is defined in the following win-
dow:

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 Defining a macro

On the left side the dialog box offers a list of the transformations that you can apply to an image.
The following is a quick description of them:
• Closure: filling in holes by smoothing over contours.
• Opening: removal of the minor artifacts with outline smoothing.
• Geodesic closing: gap filling while keeping the outlines.
• Geodesic opening: removal of the minor artefacts while preserving the contours.
• Filling: filling all gaps, whatever their size, while keeping the outlines.
• Keep edges: removal of the objects entirely contained in the field.
• Cut 2 edges: deleting objects that cut across the top or left edges of the field.
• Cut 4 edges: deleting all the objects that cut across one of the edges of the field.
• Maximum size: removal of objects that are larger than the indicated parameter, while keeping
the outlines.
The list on the right is the sequence formed by some of these transformations. To include a trans-
formation in the list, use the following procedure:
• Click in the left-hand area on the transformation you want and then click on the + button (or
simply double-click in the left-hand area on the transformation you want): the transformation
will be placed at the end of the list.
• Click on the buttons marked with an arrow to move the transformation to the place you want.
• If required by the transformation, indicate the size then validate with the <Enter> key.
The macro’s effects on the image can be viewed in real time if the switch on the right-hand side is
set to Phase or Contours.

Object separation
Separation is useful for structures for which an object count has been performed (object count or
measurement). It allows you to consider to a certain extent objects that appear to be agglomerated
as separate objects.
Three automatic separation methods are available:
• Rapid for only separating large objects;
• Standard for separating medium-sized objects;
• Fine for separating small objects.

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Application of geometric criteria
Areas makes it possible to conclude detection by applying criteria relating to the length, the width,
area, the diameter or the lengthening of the detected particles.
Menus allows you to choose the measurement and the comparison to be carried out. The limiting
value is entered in the corresponding text field.

Defining criteria

Several criteria can be combined. Generally, only the objects which satisfy all the criteria are preser-
ved : that is shown by the word "And" at the beginning of each line.
If one clicks on the button "Enlarged selection", any object satisfying the one of the criteria is pre-
served: each line begins with the word “Or”.

Saving the study

While the measurements are being taken, it is recommended to save the measured values on a re-
gular basis. The 'Save the study' item in the ‘File’ menu is used for that purpose.
The first time, this item displays the standard Windows dialogue box in which you should indicate a
directory and a file name to identify the study (the suffix ".ars" is added automatically). This name
then appears in the Areas status bar.
The same file is used for the following recordings unless it is changed explicitly by means of the
“Save as...” item.

Saved templates and files

It may be useful to define study templates that conserve in particular the definition of the phases
and the settings for the detection thereof. In order to do this, you should save the information prepa-
red in a file before taking the measurements by means of "Save study" item.
In order to make use of this template:
• Open the file with the “Open a study...” item (“File” menu). this restores the defined structures.
• Enter the characteristics specific to the new study with the corresponding item in the "Measure"
menu.
• Define a new file with the "Save study as..." item in the "File" menu.
Note: The template files can be protected from any accidental changes: in the Windows Explorer,
display the properties of the file, and tick the "read only" box.

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 4. Analysis of the sample

Sample analysis with a simple video source

Plotting a permanent test pattern

A permanent test pattern is a manual profile that is reproduced identically on all measured fields. If
such a structure has been defined at the start of the study, you just have to plot the shape to be re-
produced. Proceed as follows:
Display the “Video” page: when the field has not been measured (which is normally the case as you
define the test patterns before taking the measurements), the entire field is darkened by a uniform
grid.
Select the relevant phase from the toolbar’s pop-up menu (or from the list of “Phases” in the “Mea-
sure” menu). Choose the desired plotting tool with the corresponding toolbar button.
Plot the shape on the video image. When it is completed, the video image normally appears within
the area, with the exterior remaining darkened. Several geometric shapes can be plotted: they are
merged when the field is measured.

Taking measurements
Display the “Video” page and frame the first field to be measured.
Then use this button or the “Measure field” item in the “Measure” menu. If a permanent test
pattern has been defined, the profiles are then assigned to the field. The other phases are
detected automatically.
Move the sample and click on this button or the ‘Next field’ item in the “Measure” menu.

Repeat this alternation between Measure field / Next field to accumulate a significant amount of da-
ta.
The measured phase percentages can be checked using the “Measurement results” item in the
“Measure” menu, which displays the following palette:

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 Results expressed

The respective proportions of the different phases are shown in comparison to their respective re-
ference surfaces. In the example above, the phases are compared to the video field. If one phase is
included in another, the color of the reference zone appears on the right of the “%” symbol.
The background history of the measured fields is displayed in the “Scan” page. The image of the
fields is included if the “Keep measured images” option was activated at the start of the study.

Sample analysis with a source equipped with an indexed stage

Thanks to its indexed stage, the source informs the software of the position of the video field that it
uses during analysis to produce a mapping of the sample.

Plotting a reference area

If a phase was defined as a sample outline when defining the study, it must be plotted before any
other measurements. Select this phase from the toolbar’s pop-up menu (or from the list of “Phases”
in the “Measure” menu), and select the desired plotting tool by clicking on the corresponding tool-
bar button.
Move the stage to bring the first point in the outline into the field, and click on that point. Then go
around the sample outline, and click on a certain number of points that are more or less close de-
pending on the desired accuracy. Double-click on the same position to close the outline.
The profile obtained is displayed in full in the “Scan” page. It can be selected, and adjusted by mo-
ving one of its handles.

Taking measurements
The measurements can be taken by observing the “Video” page or the “Scan” page: the field is dis-
played in a scaled-down view and follows the stage’s movements.
Press this button or the “Measure field” item in the “Measure” menu. The phases are detected
automatically. If a reference area has been defined, only the phases detected within this area
are taken into account.
Move the sample successively to all of the locations to be measured, and press this button to take
the measurements.
During the analysis, Areas produces a mapping of the sample, including the image of the fields if
the “Keep measured images” option was activated at the start of the study.

Sample analysis with a video source equipped with a motorized stage

A motorized stage allows the software to program the sample’s movements, and the position of the
video field in the sample is known.

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When the video source is equipped with such a stage, the “Follow pre-defined scan” box in the
“New study” dialog box is checked. If this box is not checked, Areas is used as described in the pre-
vious paragraph. When the box is checked, some additional functionalities are available as descri-
bed below.

Defining the scan

The scan is defined by a rectangular or circular area that the software will scan to successively ana-
lyze all of the fields that it contains.
The following dialog box (“Define scan…” in the “Measure” menu) is used to choose the shape and
size of this scan:

The area thus defined can be scanned in several different ways with the options in the two other
frames. You can, for example, define an exhaustive scan of the sample (check the “Include periphe-
ral fields” and “Joining fields” boxes) or prefer a more rapid analysis (by defining the disjoint fields
or by letting the system choose fields at random).
The zone to be analyzed is represented in the “Overview” page. The size and position of the zone
can be adjusted with the mouse.

Previewing the sample

Areas allows you to preview the sample before the actual analysis in order to locate any areas of
interest in the overview. In order to do this:
• Choose a low magnification lens on the microscope and select the corresponding calibration
from the list of calibrations in the “Measure” menu, and then

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• Position the scanning area around the area to be analyzed (by moving and resizing its represen-
tation in the “Scan” page), and
• Select the “Acquire preview” item from the “Measure” menu. The system then produces an im-
age of the sample.
• Return to the lens to be used for the analysis and select the corresponding calibration from the
list.
The sample image is displayed as a watermark in the “Scan” page. In particular it allows you to plot
the sample outline, provided that a phase of that type was declared when the study was defined.

Taking measurements
The measurements can be taken by observing either the “Video” page or the “Scan” page.
Select the “First field” item from the “Measure” menu (or click on the button opposite while
holding down the <Shift> key): the stage moves towards the first scanning field.
To analyze the first fields step-by-step:
Use this button or the “Measure field” item in the “Measure” menu. The phases are detected
automatically.
Click on this button or the ‘Next field’ item in the ‘Measure’ menu: the stage moves to the
next location to be analyzed.
Measure a few fields in this way to check that the settings made are satisfactory, then:
Click on this button: the rest of the scanning process is performed automatically.

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 5. Overview of sample

The “Scan” page presents an overview of all of the measured fields. The detected phases are repre-
sented in a scaled-down view. They are superposed onto the image that was present under the ca-
mera when the measurements were taken (if the “Keep the measured images” box was checked
when the study was defined).

The boxed field is the "active" field, whose data is also displayed on the "Video" page. The mouse
can be used to modify the objects in this field.
In order to change the active field, use the "Previous field" and "Next field" options in the "Measure"
menu or the corresponding buttons in the toolbar or click on the desired field while at the same time

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holding down the <Shift> and <Ctrl> keys on the keyboard.
When the video source is equipped with a stage that transmits its position to the microcomputer
(motorized or indexed stage), the background history is replaced by a mapping of the sample: Any
preview and the scanning area are then displayed here. The scanning area can be moved and de-
formed with the mouse so that it can be adjusted to the area of interest on the sample.
If the stage is motorized, it can be moved using the “Previous field” and “Next field” options in the
“Measure” menu or the corresponding buttons in the toolbar or click on the desired location while at
the same time holding down the <Shift> and <Ctrl> keys on the keyboard.
The overview can be displayed in a separate window and thus remain visible even when you are
working on the other pages of Areas: for that, you can use the “Display in window” option in the
“Results” menu or the corresponding keyboard shortcut, the <F12> key.
This button located on the right of the toolbar button symbolizes the overview: it displays it in a
window just like the previous function, except in the “Report” page: it is then used to include the
overview in the printed report.

Exports
• Saving the preview for a later analysis: use the “Export preview ” item in the “File” menu.
The preview is saved in the “Microvision Cartography” format. The mappings can be analyzed
by Areas or another measurement software application by using the “Read a mapping” option in
the list of video sources.
• Saving the measured images: use the “Export overview ” item in the “File” menu.
The images are saved in a single file in the “Microvision Cartography” format, which retains all
of the acquired data (especially calibration and the field positions). The mappings can be re-
loaded in Archimed for annotation, integration into a report or extraction of individual images.
• Transformation of the history into a single image: select the "Frame" tool in the "Edit" menu,
then select the required zone. The "Copy" option allows you to transfer the selected portion to
other software.

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 6. Measurements table

While the fields are being analysed, Areas creates a table that groups together the values measured.
The table is displayed by selecting the corresponding tab.

Each object occupies a line and is described by the analysis field number, the name of the phase to
which it belongs and by the result of the measurements taken.
The keys and measurements included in the table are defined using the “Table properties…”
item in the “Results” menu, or the button on the tool bar shown opposite.
The “Keys” tab in the dialog box presents the localization and identification information for the mea-
sured objects.

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An object is always part of a field, whose order number may be displayed. If the field corresponds to
an image file, it may be important to indicate its name in the table.
An object always belongs to a phase, whose name may be indicated. If this phase was defined as
being included in another phase, the object is therefore included in one of the objects of that other
phase. Displaying the object number and that of the containing object allows you to identify them.
The “Measures” tab presents nine geometrical parameters taken from the objects themselves:
• The X-axis and the Y-axis and the coordinates of the centers of gravity for the objects.
• The length and the width are derived from the object inertia. They are adapted for convex ob-
jects.
• The median and the thickness are adapted for fine objects. The median is the length of all
branches of the object; the thickness is the mean thickness of the branches.
• The diameter is that of the circle with the same surface as the object.
• The perimeter is the length of the object’s outline.
• The surface is deduced from the number of pixels in the object.

If a phase is used as a reference area for another phase, Areas gives you the possibility to include in
the table statistics regarding the number and surface area of the objects contained in each object

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present in the table.
You can choose the accuracy of the values from this window by clicking on the corresponding pull-
down menu.
The “Phases” tab allows you to select the phases displayed in the table. If a phase is present, its ob-
jects can be listed individually or grouped by measurement field. In the second case, the sum of the
perimeters and surface areas are calculated.

A few restrictions apply when a phase hierarchy has been defined: when you display the individual
list of the objects in a phase, the same organization applies to the phases it contains. Conversely, if
you wish to group the values for a phase, the values for its reference structure must also be grou-
ped.

Object sorting
Areas provides two methods of displaying the objects plotted and detected. Depending on the arti-
cle checked in the “Results” menu:
- the objects can be “sorted by phase”, which is practical for comparing the measurements of seve-
ral objects from the same phase,
- the objects can be “sorted by field”, and then within each field they can be sorted by measurement
area: this compares the measurements of an object with those of the object containing it.

Exports
Exporting the results consists in formatting the results obtained by Areas so that they can be used
by external software applications (spreadsheet programs in general). Two techniques are available:
• Via the clipboard: select the block of cells. When it is highlighted, select the “Copy” option in the
“Edit” menu. Activate the destination software application and paste at the desired position.
To select entire lines, click and drag in the legend columns. To select entire columns, click and
move in the heading lines. To select the entire table, click on the top left corner of the table.
• Via a “text” format file: in the “File” menu, use the “Export” sub-menu, then the “Measurement
table…” item.
IMPORTANT NOTE: Exportation must not be confused with saving a study. A study file contains
the measurements and their environment, but can only be read by Areas. An exported file only

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 contains the values but can be read by another software program. It is always preferable to save
the study, as you can then extract the values in order to export them, whereas the reverse is not
possible.

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 7. Statistics and Graphs

The “Results” page presents four documents:

• The surfaces table which has as many lines as there are measured fields. The columns contain
the surfaces measured on the different phases.
• The statistics summarize the values of the geometrical parameters for the whole study.
• The distribution histogram of one of these parameters and the list of calculated values.

The results of the surfaces table can be expressed in real units (surface of each of the pha-
ses) or as a percentage of the surface of the reference area. This choice is made using the

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“Displayed results” item in the “Results” menu, which displays the following dialog box:

Choice of columns displayed in the surfaces table,

and level of accuracy of the displayed values

The statistics refer to the measurements presented in the measurements table. The values
are displayed with the same level of accuracy.
A particular measurement (length, width, median, thickness, diameter, perimeter or surface) can be
analyzed individually thanks to a distribution histogram: size classes must be defined for the mea-
surement in question and the phase(s) to be taken into account must be selected. The histogram is
presented in the form of a “bar” graph. The number of objects in each class can also be displayed.

It is possible to display the normal law corresponding to the distribution of the measurement in the
defined classes by checking the corresponding option in the lower part of this window.
Other plotting options (color of the bars and the normal law, graph gridline, curve thickness) can
also be chosen under the histogram.
The distribution histogram is defined using the “Histogram properties” item in the “Results”
menu, which displays the following dialog box:

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You can allow Areas to adjust each of the parameters as best it can by checking the “Auto” boxes.
These buttons in the tool bar represent the four documents. In the “Results” page,
they are used to display or hide them. In the “Report” page, they are used to select
whether or not they are included in the printed document. In the other pages, these
buttons are used to display the tables in a separate window.

Exports
• To presentation software via the clipboard: Click on the title bar of the required document. When
it is highlighted, select the “Copy” option in the “Edit” menu. Activate the destination software
application and paste at the desired position.
• to a spreadsheet programme via a "text" format file: use the “Export surfaces table” or “Export
statistics” items in the “File” menu.

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 8. Page layout and Report print-out

The "Report" page shows the measurements report exactly as it will be printed:

The page layout of this document is entirely customizable: size and contents of the header
and footer, order and title of the printed documents. The "Report settings..." item in the "Re-
sults" menu is used for this purpose.
Three types of headers are available:
• a standard header, not requiring any settings, which automatically includes the name of the
software followed by the study reference.

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• a customizable header for which you can define the height, the title and a logo that you will have
already placed in the clipboard.
• A blank header for printing the report on pre-printed paper. You then only set the height of the
space to be left blank.
The footer may include the software reference and page numbering or a given height may be left
blank for use with pre-printed paper.

Definition of the header and footer

The second tab is used for defining the contents of the report:

The list shown allows you to choose the documents to be included in the report and to determine
the order and title.
These buttons located in the toolbar allow you to quickly include the cor-
responding documents in the report without opening the dialog box.

Exporting to PDF format

If Adobe Distiller is installed on the workstation, the report can be exported in “PDF” format, which
allows you to display it on a workstation not equipped with Areas.

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 9. Secure operating modes

For routine use of Areas, it may be interesting to freeze the settings made in order to prevent ma-
king any accidental changes. Areas provides the following three operating modes:
• the “Administration” mode is the normal operating mode in which all software functions can be
accessed.
• The “Operations” mode is a secure mode in which all routine operations are possible, whereas
certain functions are no longer accessible.
• The “Supervision” mode is a secure mode in which the adjustments remain accessible, but are
consigned in a log-file. Accesses to files are restricted, and also consigned in the log-file. This
mode is defined by a distinct software component, separately sold.

The operating mode shown in the "?" menu

The “Security settings...” item allows the administrator to define the software operating mode and to
protect this choice with a password. You can also define which routine operations are authorized.

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