Nikon NIS-Elements User Guide
NIS-Elements
M378 E 07.5.NF.5
Advanced Research
User’s Guide
(Ver. 2.34)
Thank you very much for choosing Nikon.
This manual explains installation and use of the NIS-Elements Advanced Research. For
trouble-free operation, read this manual before using the program.
No part of this manual may be reproduced without Nikon’s permission.
The content of this manual is subject to change without notice.
Nikon has carefully prepared this manual. However, we make no expressed or implied
warranty of any kind and assume no responsibility for such errors or omissions.
Be sure to read the instruction manuals for the microscope and PC you plan to use with the
NIS-Elements Advanced Research.
Trademarks:
Microsoft® and Windows® are either registered trademarks or trademarks of Microsoft
Corporation in the United States or other countries.
Products and brand names are trademarks or registered trademarks of their respective
companies.
The “TM” and ®marks are not used to identify registered trademarks and trademarks in this
manual.
To run NIS-Elements Advanced Research optimally, the following specifi cations are
recommended.
Recommended PC Environment:
CPU: Pentium IV, 3.2 GHz or faster
RAM: 1GB or higher
Operating system: Windows XP SP2 (English)
Hard disk space: 600MB of available hard disk space for installation
Display settings: 1280 x 1024 (True Color mode)
User rights: Administrators for installation and operation
*Operation cannot be guaranteed on all computer models. For futher information, contact
your nearest Nikon representatives.
Table of contents
INSTALLATION AND STARTUP
NIS-Elements Installation ................................................................7
APPLICATION APPEREANCE
NIS-Elements Screen .................................................................... 15
Layout Manager ......................................................................... 19
Organizer ................................................................................. 25
SETTING THE HARDWARE UP
Cameras .................................................................................. 33
Confi guring Attached Hardware ....................................................... 35
CAPTURING IMAGES
Images Capturing ........................................................................ 43
Time Lapse Acquisition ................................................................. 45
Multipoint acquisition .................................................................. 47
Z Series Acquisition ..................................................................... 49
Fluorescence acquisition ............................................................... 51
Capturing to Ring Buffer ............................................................... 53
DOCUMENTS, ARCHIVING
NIS-Elements Document Structure ................................................... 57
Working with Documents ............................................................... 61
IMAGE ANALYSIS
Histogram and Look Up Tables ........................................................ 67
Binary Editor ............................................................................. 73
Measurement ............................................................................ 77
Object Count ............................................................................ 81
Time Measurement ...................................................................... 85
Mathematical Morphology Basics ..................................................... 91
How to create a simple macro? ...................................................... 101
Creating Reports ....................................................................... 105
CUSTOMIZATION
Modifying Main Toolbar ................................................................. 113
Command Line Options ................................................................. 117
ADDITIONAL MODULES
Database Module ........................................................................ 121
Extended Depth of Focus Module ..................................................... 131
ND Experiments ......................................................................... 137
Deconvolution Module .................................................................. 141
The 2D RT Deconvolution Module ..................................................... 143
Stage XY Module ......................................................................... 147
Stage Z Module .......................................................................... 157
90i Module................................................................................ 163
TE2000 Module .......................................................................... 167
Coolscope Module ...................................................................... 171
Nikon MM 400/800 Microscope ........................................................ 175
Nikon Eclipse LV Series Microscope ................................................... 179
Nikon AZ100 Microscope ............................................................... 187
Chapters and paragraphs marked by this symbol describe features available only in the
Advanced Research version of NIS-Elements.
Installation and Startup
Installation
NIS-Elements Installation
Quick Start
The CD-ROM
Content
Installation
Quick Start
- Insert the installation CD in the CD-ROM drive. A splash screen automatically appears.
- Install the selected NIS-Elements software version, additional modules, and device
drivers.
- Plug in your HASP key into the USB port of your PC.
- Run NIS-Elements
The CD-ROM Content
The CD-ROM contains the NIS-Elements software itself, Windows system drivers for all
supported cameras, drivers and utilities for HASP, documentation in PDF format, a sample
image database, and sample image sequences for additional modules.
The installation process
Note that you have to possess the administrator rights to your computer to be able to install
NIS-Elements successfully. When the installation CD is inserted a splash screen appears.
Specifying
the software
version
Select the software version to be installed. Select the one you‘ve got the license for and that
is properly coded in your HASP hardlock key. The welcome dialog box appears. Click Next
to continue.
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Installation
Installation
directory
Defi ne the folder where the NIS-Elements software should be installed. We recommend to
use the predefi ned directory. If you want to change the directory, press the Browse button
and select a new one, otherwise click Next .
Selecting
cameras
Now select the cameras you want to use with NIS-Elements.
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Selecting
modules
Installation
If your licence contains some additional modules besides the NIS-Elements base software,
please select them in this window.
Selecting
devices
Note:
Any module selected will be installed along with NIS-Elements automatically. However, you
might not be licensed to use it. The module will run after you get a corresponding code
registered in your HASP key.
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Installation
If your licence contains some device controllers listed in this window, please select them.
Finish the installation by clicking the Install button.
The program
group
Additional
installations
The Setup creates the NIS-Elements program group with the following items: HASP key information, NIS-Elements shortcut, Modify Installation (for adding hardware drivers, modules,
etc.), Uninstall procedure, and the Send Info Tool. A shortcut is created on the desktop. These
changes affect all user profi les of your local Windows system.
Note:
Clicking the Uninstall command deletes all installed fi les from disk, and removes the NIS-
Elements program group from Windows Start menu as well as the desktop icon.
Additional Module/Device installation
You may need to install a device or additional module after the NIS-Elements main system
installation.
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Installation
- Go to Start menu>Programs>NIS-Elements program group.
- Select the Modify Installation command.
- Follow the install shield instructions.Check the checkboxes by the items you would like to
add.
- Finish the installation.
Installing sample database
Software copy
protection
Sample Database installation
If you chose to install the Sample Database, a new subdirectory „Databases“ is created
in NIS-Elements installation directory (e.g. C:\Program fi les\NIS-Elements\Databases\...).
The „Sample_Database.mdb“ fi le is copied in there along with database images (stored in
subdirectories). An administrator username/password to access this database is set to:
- Username: „sa“
- Password: „sa“
The software copy protection
The NIS-Elements software is delivered with a HASP hardware key.
The HASP key contains information about the SW licence and allows
users to run the corresponding software. Please connect the
USB HASP after NIS-Elements installation. The utility called
„HASPinfo“ (Help menu) is installed to the NIS-Elements
directory. It enables the user to view information about
the actual software licence:
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Installation
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Application Appereance
NIS-Elements Screen
NIS-Elements Screen
Screen items
The following items appear on the screen:
- The menu bar containing pop-up menus with sets of commands.
- Two main toolbars (horizontal and vertical)
- Document toolbars (right and top) enabling to customize the images view. See its
description in the Document structure chapter.
- Docked control windows - see more description of docking windows in the Layout
Manager chapter.
- The status bar displaying useful information.
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NIS-Elements Screen
Main toolbars
Horizontal toolbar
- Open fi le shortcut.
- Save fi le shortcut.
- Save Next shortcut.
- Print Image shortcut.
- Undo button.
- Redo button.
- Show live window displays a new document window with live signal from camera.
- RAM buffer ON - please see the Capturing to ring buffer chapter.
- Capture to RAM buffer - please see the Capturing to ring buffer chapter.
- Background correction ON is a shortcut to the Acquire>Backgroun Correction
ON/OFF command.
- Explore optical confi gurations button shows the optical confi gurations manager.
- New optical confi guration runs the optical confi guration wizard.
Vertical toolbar
- Pointing Tool enables to drag the image.
- Magnifi er Glass - interactive magnifi er tool to examine image details.
- Length measurement tool for interactive length measurements.
- Area measurement tool for interactive area measurements.
- Taxonomy tool for sorting objects in the picture into classes.
- Counts tool for counting objects in the picture.
- Radius tool for measuring radius of a circle.
- Semiaxis tool for measuring semiaxes of an ellipse.
- Angle tool for measuring angles.
- 3D Measurement tool measures length accross Z sequences (req. EDF module).
- Insert Arrow tool for inserting annotations.
- Insert Text tool for inserting text annotations.
- Capture Time Lapse automatically or manually.
- Capture Z Series automatically or manually.
- Capture Multichannel automatically or manually.
- Capture Multipoint automatically or manually.
- Real Time EDF performs Z series acquisition and EDF in one step (req. EDF)
- Copy copies the current image to memory.
- Paste As New Image creates a new document and inserts the image from memory.
- Crop tool for cropping images.
- Run Macro command runs the current macro.
- Close All documents shortcut.
- General Options
- ToolBar Setup
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Status bar Status bar
The status bar at the bottom shows the following information (from left to right): available
views, a type of selected camera, the function corresponding to the last command used,
active objective name, and current coordinates of a stage and a Z-drive (if connected).
NIS-Elements Screen
Page 17
NIS-Elements Screen
Page 18
Displaying
docking pane
Layout Manager
Layout Manager
There can be a number of control windows (Camera Settings, Measurement, Histogram,
LUTs, etc.) displayed within the application window in several different ways, fl oating., docked
inside a docking pane, in tab or caption style..
To display a docking pane
Docking panes are empty square spaces inside the application window, where you can place
(„dock“) the control windows. They can help to keep the screen „tidy“. There is one docking
pane available on each side (Top, Right, Bottom, Left).
- Go to the View>Docking Panes submenu and select the pane you would like to display.
- The docking pane appears, either empty or with some window(s) docked.
- Repeat this task to display more panes.
Hiding
docking pane
The same submenu can be also displayed by right-clicking into the empty application scre-
en.
To hide a docking pane
Either click the arrows in the top left
corner, or double click the empty pane
(not the docked control window). The
pane minimizes to a stripe by the edge
of the application. It can be recalled to
its original size by double clicking it.
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Layout Manager
Shrink/Expand
docking panes
If you would like to close the pane completely, minimize it and press the cross button, or you can right click
the pane and unselect the Docking View option.
To shrink/expand docking panes
Having more docking panes opened, a
situation where there is not enough room for
the control windows can occur. In that case,
the Shrink and Expand commands shall be
used.
- Right click the pane you would like to
shrink/expand.
- A context menu appears.
- Select the Expand/Shrink command.
Control
windows
The commands Shrink/Expand Top, Right, Bottom, Left are available. When one of the panes
shrinks, the neighbouring pane expands to the emptied corner and vice-versa.
Control windows
The following control windows can be displayed within the application screen. They can be
fl oating, or docked inside the horizontal or vertical docking panes:
- 3D Measurement* (horizontal, req. EDF)
- Auto Capture Folder (horizontal)
- Camera Settings* (vertical)
- Filters and Shutters* (vertical)
- Histogram (vertical)
- Intensity Profi le (horizontal)
- LUTs (vertical)
- Lamp* (vertical)
- Measurement (horizontal)
- Microscope Control Pad* (vertical)
- Nosepiece* (vertical)
* - this control window is optional. A proper software licence or a correct device connected is
required in order to display it.
- Object Count (horizontal)
- Opened Views (horizontal, vertical)
- Preview (vertical)
- ROI Statistics (vertical)
- RT Deconvolution* (vertical)
- Time Measurement* (horizontal)
- View Synchronizer (vertical)
- Virtual Joystick* (vertical)
- Volume Measurement (horizontal,
vertical)
- Z Profi le* (horizontal, vertical)
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Layout Manager
Displaying
control window
Closing control
window
Caption styles
To display a control window
- Go to the View>Controls
submenu and select the
desired control window.
- The control window
appears fl oating on the
screen.
- To dock (and undock) it,
double click its caption.
It is also possible to display a control window docked. Right click inside a docking pane
and select the one of your choice. If the window is already opened somewhere (e.g. in the
opposite pane or fl oating), it closes and moves to the new destination.
To close a control window
- Click the „cross“ button on the right side of the active window caption.
- If the window is docked, you can also right click its caption and uncheck the appropriate
window.
- The control window closes.
Tab or caption style?
More control windows can be docked in the same place while only the front one is being
visible. There are two styles of displaying these windows, Tab and Caption.
Tab Style
- Besides the current control
window, the other window
tabs are visible.
- Switching the windows is a
one click operation.
Caption Style
- All docked windows except
the current one are hidden.
- The switching and undocking
of windows is done via the
menu that appears when you
click the arrow button.
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Layout Manager
Managing
layouts
Creating new
layout
To manage layouts via the layout manager
The application can operate in two modes: supporting layouts or not.
To switch the layouts mode ON/OFF, reach the General Options tab
by double clicking the NIS-Elements caption. In the Appereance section, there is a check box
that enables/disables the mode.
When you start the application with the Layouts mode ON, blue tabs representing active
layouts appear in the bottom left corner. The Full Screen and Docked Controls layouts are
placed by default. Other layouts can be added and managed via the Layout Manager.
If the „Read Only Layouts“ box is checked, no layout changes are saved during work or on
exit.
To create a new layout
- Modify the current layout to suit your concept of work.
- The asterisk appears next to the layout name (to indicate it has been modifi ed).
- Right click the layout tab and select the Save Current Layout As command.
- Write the new layout name and confi rm it by OK.
- A new tab appears and the layout is saved to the list of layouts.
If you do not need to create a new layout but would like to save the changes made, just right
click the current tab (asterisk-signed) and select the Save command from the menu.
Discarding
changes
Page 22
To reload previous layout settings
Unwanted changes of a layout may be made. Mostly, it can be fi xed by the Reload comma-
nd.
- Right click the asterisk-signed (recently modifi ed but not saved) tab and choose the
Reload command.
- The application restores the last saved state of the layout.
Layout Manager
Using layout
manager
Layout manager
Right click any layout tab and select the Layout Manager command. The Layout Manager
appears.
- The check boxes on the left indicates the layout visibility (displayed/hidden)
- The Activate button makes the selected layout active (current)
- The Load Default button has the same functionality as the Reload command described
above. Except when applied to the Full Screen and the Docked Controls layouts where it
loads the original settings - so they look just the same as after the program installation.
- The Delete button deletes the selected layout. The fi rst two layouts cannot be deleted.
- Advanced settings enable to run a command or a macro right before and after a layout
change. It can be assigned to one or to all the layouts.
- The OK button stores all changes and closes the Layout Manager.
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Layout Manager
Page 24
Organizer
Organizer
Organizer
structure
Files view
Apart from the main application mode used for capturing and
image analysis, NIS-Elements provides a special Organizer
mode.
Organizer was designed to ease the work with image fi les
and databases. Clicking the Organizer button located in the
upper right corner of the NIS-Elements application window
or pressing F10 activates Organizer.
The screen is primarily divided into two identical panes. Each pane can be switched into two
modes: the Files mode and the Database mode. To switch from one pane to the other one
use „Next Pane“ command from the View menu. To copy fi les from one pane to the other one
simply drag selected images to the other pane.
- This button switches the pane to show a directory tree and images from the selected
folder (and its subfolders, when selected - see below). It is called the Files view .
- This button switches the pane to show the database structure and lists images
from the currently selected database table. This is called the Database view .
Features available in the Files view
- This button toggles the display of the directory tree. You can switch it off to get
additional space to display images.
- In this combo box it is possible to set the fi le type to be displayed.
You can select only a particular extension or show all fi les.
- If this check-box is selected all images from the included subfolders are
shown.
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Organizer
Database view
Features available in the Database view
- This button toggles display of the database navigation and detailed information about
the selected image. You can switch it off to get additional space to display images.
- This combo-box displays the active connection point or enables to
select another defi ned connection point.
- This combo-box selects the database table and also indicates the current
table.
Filtering images
Page 26
Image fi lter
Both views (File and Database) have an option to use fi lters . It enables you to display only
such images, that match the criteria given.
- This button activates the fi lter.
- Pressing this button invokes the fi lter setup dialog box.
The fi lter can be used in two modes:
Organizer
Basic fi ltering
Advanced
fi ltering
Basic mode
This mode enables you to view fi les that match one defi ned condition.
Advanced mode
This mode enables you to defi ne two conditions with a relationship defi ned between them.
Either select OR to display fi les with the properties matching at least one given condition, or
select AND to display fi les the properties of which match both conditions at once.
First, select the fi eld, where NIS-Elements should search for a given expression. When using
a fi lter in the Files view, there are fi elds from fi le properties listed. In the Database view, the
listbox shows the names of fi elds from the currently selected database table.
If a selected fi eld is of a numerical type (e.g. Size, Calibration, File date etc.) you can specify,
whether you want to fi nd the exact value or a value in a given range (both displayed in the
picture above). This is selected by the Condition type radio button.
- Anywhere - If a given sequence of characters is found anywhere in the sequence of
characters in the fi eld, the system will evaluate it as a match. E.g. you have entered set
to the values edit box. The fi lter will select records with fi eld values: set , re set , set tings,
pre set ed...
- Exact - If the given sequence of characters exactly equals to the content of the fi eld, it
is evaluated as a match. E.g. if set is entered, fi elds containing the set value will only
match.
- Start - If the entered string is found at the beginning of a fi eld, it is displayed by fi lter. E.g
if set is entered, fi elds containing set , set ing set up are selected.
- All letter strings - It is possible to search for more expressions. These should be entered
separated by commas. If you want to enter an expression with a space, insert it into
Page 27
Organizer
quotes. If this option is selected, only records in whose fi elds all of those expressions
(anywhere) appear are selected.
- Any letter string - This option is for entering multiple expressions as above, but this time
every fi eld with an occurrence of at least one from the given expressions is matched.
Operations with
images
Displaying
thumbnails
Operations with images
To open an image from the Files view, double click it. NIS-
Elements will display it in the main mode. To select multiple
images, either click on the fi rst and the last image holding
the Shift key (continuous group selection) or click individual
image names with the Ctrl key down to select more fi les that
do not appear together.
You can copy one or more selected images from one folder
to another only by dragging and dropping. This can be used
to ease inserting of images to the database too. Simply drag
the image from a folder and drop it onto the pane, where the
database table is opened. To delete selected images press
the Delete key.
All those operations and some other can be invoked also from the context menu, which
appears each time you right click on the image thumbnail:
Thumbnail displaying options
You can adjust the way images are shown in the panes. The
menu can be invoked in the main bar, where you can select the
size of displayed image thumbnails. Selecting the Details with
preview will display only one image per row with additional information about the image (image properties, if the images are in
folder or database fi elds, when viewing database records.)
Page 28
There is a possibility to rotate images which have wrong orientation. It doesn‘t affect just the display, but changes the underlying
image data too.
- Rotates image (or more selected images) left.
- Rotates image (or more selected images) right.
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