User manual | Imaging Software NIS-Elements

Imaging Software NIS-Elements
Nikon offers total software solution covering image capture, archiving, and analysis
NIS-Elements is an integrated software imaging platform developed by
Nikon to achieve comprehensive microscope control, image capture,
documentation, data management and analysis.
NIS-Elements handles multidimensional imaging tasks flawlessly with
support for capture, display, peripheral device control, and data
management & analysis of images of up to six dimensions. The system
also contributes to experiment efficiency with a database building
feature developed to handle archiving, searching, and analysis of large
numbers of multidimensional image files.
Unified control of the entire imaging system offers significant benefits
to users for cutting-edge research, such as live cell imaging.
Why NIS-Elements?
As a leading microscope manufacturer, Nikon realizes the
importance of providing its customers with system-based
solutions to free the user to focus on the work and not the
complexities of the microscope. NIS-Elements was designed
with this in mind. Never before has a software package
achieved such comprehensive control of microscope image
capturing and document data management.
Microscopes
Total Imaging Solution
Digital Cameras
Software
In designing and bringing to market the most
technologically advanced optical systems, Nikon has
worked very hard to provide a “total imaging
solution” that meets the ever-evolving demands of
the microscope user.
•Highest Quality Optical Performance
The world-renowned Nikon CFI60 infinity optical system effectively set a new standard for optical quality by providing longer working
distances, higher numerical apertures, and the widest magnification range and documentation field sizes.
As a leader in digital imaging technology, Nikon recognized the importance of adapting its optics to optimize the digital image. Nikon’s new
objectives and accessories are specifically engineered for digital imaging, with exclusive features, such as the Hi S/N System, which eliminates
stray light and provides unprecedented signal-to-noise ratios.
Because what you see depends greatly on the quality of your microscope, we strive to power our microscope systems with optical technologies
that are nothing but state-of-the-art.
•Diverse Line of Powerful Digital Cameras
The NIS-Elements suite is available in three
packages scaled to address specific application
requirements.
Image capture has become a high priority in microscopy and the demand for products that deliver high quality and versatile functionality has
grown considerably in recent years. In accordance, Nikon offers a full line of digital cameras, addressing the varied needs of microscopists in
multiple disciplines. Each Nikon digital camera is designed to work seamlessly with Nikon microscopes, peripherals, and software. With Nikon
Digital Sight (DS) series cameras, even novice users can take beautiful and accurate microscopic images. For the advanced researcher, hiresolution image capture and versatile camera control is fast and simple. Together with Nikon’s new software solutions, image processing and
analysis have reached new levels of ease-of-use and sophistication.
•Intelligent Software Solutions
The most sophisticated of the three packages, NIS-Elements
AR is optimized for advanced research applications. It
features fully automated acquisition and device control
through full 6D (X, Y, Z, Lambda (Wavelength), Time,
Multipoint) image acquisition and analysis.
NIS-Elements BR is suited for standard research applications,
such as analysis and photodocumentation of fluorescent
imaging. It features acquisition and device control through
4D (up to four dimensions can be selected from X, Y, Z,
Lambda (Wavelength), Time, Multipoint) acquisition.
NIS-Elements D supports color documentation requirements
in bioresearch, clinical and industrial applications, with basic
measuring and reporting capabilities.
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Designed to serve the needs of advanced bioresearch, clinical, industrial and documentation professionals, NIS-Elements provides a totally
integrated solution for users of Nikon and other manufacturers’ accessories by delivering automated intelligence to microscopes, cameras, and
peripheral components. The software optimizes the imaging process and workflow and provides the critical element of information
management for system based microscopy.
Multi-layer Document Structure
NIS-Elements uses a sophisticated image documentation structure making it possible
to achieve non-destructive archiving of image data including annotation (arrows,
lines, text notes), measurement data, binary data for storing results of threshold or
classification processes, and meta-data information for recording acquisition and
device conditions at the time of image acquisition.
Annotations
Binary
Color
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Realizing a smooth flow from image capture to process and me asurement
Image Acquisition
Optical Configuration
Microscope parameters, such as fluorescence filter and
shutter combinations, can be saved and displayed as icons
in the tool bar, allowing one-click setup. Setting up a CCD
camera, applying shading compensation to each objective
lens, and saving calibration data is also possible.
Large Image Stitching
AVI Capture
This tool allows composition of large-area images with high magnification. Ultra
high-resolution images can be stitched automatically from multiple frames
through use of a motorized stage. NIS-Elements uses special algorithms to
assure maximal accuracy during stitching. The user can also capture and stitch
frames by moving the microscope stage manually.
This tool allows acquisition of images in AVI file format.
View
Image acquisition screen
nD Viewer (Multidimensional
image display)
Diverse Dimensional Acquisition
Multichannel Image
Z-series
Images using defined filters can be
captured to view in various light
wavelengths. Simply define the color
of channels and the optical
configuration that is to be used for
capturing the set of images.
Images at different Z-axis planes can be captured with a motorized Z-Focus
control. NIS-Elements supports two methods of Z-axis capture: Absolute
Positioning and Relative Positioning.
Easy-to-use parameters for multidimensional image
operation are located on the frame of the screen.
Time
Multipoint
Z-series
Channel
View Synchronizer
Single-color images
The View Synchronizer allows for the comparison of two or
more multidimensional image documents. It automatically
synchronizes the views of all documents added.
All-color merged image
Specified-color merged image
Experiment data information
Time Lapse
Multipoint Experiments
The sophisticated but user-friendly timelapse process enables the staggering of
image capture simply by defining interval,
duration, and frequency of capture.
With the motorized stage installed, it is possible to automatically capture images
at different XY and Z locations.
Sequential Data Processing
Various image views can be selected to study captured data.
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15 sec.
30 sec.
Volume rendering
Orthogonal image
Tiled image
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Time Measurement
RAM Capturing
Morphology
Time Measurement records the average pixel intensities within
defined probes during a time interval and can be performed on live
or captured data sets. Time measurement also allows for real-time
ratios between two channels.
RAM Capturing enables the recording of very quick sequences to
capture the most rapid biological events by streaming data directly
to the computer’s video memory.
NIS-Elements offers a rich spectrum of mathematical
morphology filters for object classification. Morphology
filters can be used to segment binary and grayscale
images for measurement analysis purposes. Various
morphometric parameters mean image processing is
easier than ever.
Original
ROI statistics
Statistics pertaining to area and
brightness of defined region of
interest (ROI) can be easily
collected. Results can be saved as
an Excel file.
It is also possible to compare ROI
analysis data of different
channels.
Contour
Threshold
Zones of Influence + Source
•Basic morphology (erosion, dilatation, open, close)
•Homotopic transformations (clean, fill holes, contour, smooth)
•Skeleton functions (medial axis, skeletonize, pruning)
•Morphologic separation and others
Image Processing
Color Adjustment
Image Arithmetic
contrast/background subtraction/component mix
A+B/A-B/Max/Min
NIS-Elements is suitable for hue adjustment, independently for each
color, and converts the color image to an RGB or HSI component.
NIS-Elements performs arithmetic operations on color images.
Measurement
Interactive Measurement
Classifier
NIS-Elements offers all necessary
measurement parameters, such as
taxonomy, counts, length, semiaxes,
area and angle profile. Measurements
can be made by drawing the objects
directly on the image. All output results
can be exported to any spreadsheet
editor.
Classifier allows segmentation of the image pixels according to
different user-defined classes, and is based on different pixel features
such as intensity values, RGB values, HSI values, or RGB values
ignoring intensity. The classifier enables data to be saved in separate
files.
Merge Channels
Filters
smoothing/sharpness/edge detection
NIS-Elements contains intelligent masking filters for image smoothing,
sharpness, edge detection, etc. These filters not only filter noise, but
also are effective in retaining the image’s sharpness and detail.
Multiple single channel images (captured with different optical filters
or under different camera settings) can be merged together simply by
dragging from one image to another. In addition, the combined
images can be stored to a file while maintaining their original bit
depths or, optionally, can be converted into an RGB image.
Automatic Measurement
NIS-Elements enables automatic measurement
by creating a binary image. It can automatically
measure length, area, density and colorimetry
parameters sets, etc. About 90 different object
and field features can be measured
automatically.
Object counting
Complicated procedures such as Thresholding, Morphology and
Restrictions are pulled into one control window, simplifying the
measurement process and boosting ease of use. Settings are applied
to measurement results in real time.
Before using the edge detection filter
After using the edge detection filter
Report Generator
Profile
Five possible interactive line profile measurements provide consecutive
intensity of a sourced image along an arbitrary path (free line, twopoint line, horizontal line, vertical line and polyline).
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Report Generator enables the user to create customized reports
containing images, database descriptions, measured data, user
texts, and graphics. PDF files can be created directly from NISElements.
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Various convenient plug-ins for advanced imaging and analysis capabilities
Multidimensional Acquisition (4D/6D)
2D Real-time Deconvolution
3D AutoQuant® Blind Deconvolution
NIS-Elements can combine X, Y, Z, Lambda (wavelength), Time and Multi-Stage
points within one integrated platform for multidimensional imaging. All
combinations of multidimensional images can be combined together in one ND2
file sequence using an efficient workflow and intuitive GUI. The user can easily
choose the proper parameters for each dimension and the software and hardware
will work seamlessly together to provide high quality results. Results may be
exported into other supported image and video file formats.
The real-time 2D deconvolution module
(from AutoQuant ®) allows the user to
observe live specimens with less out-offocus blur. It allows faint biological
processes to be observed that may
otherwise be missed and increases
observed signal-to-noise ratio.
The haze and blur of the image that can occur
when capturing a thick specimen or a
fluorescence image can be eliminated from the
captured 3D image.
T, XY, Z, λ simultaneous acquisition
Calcium & FRET
Before deconvolution
This plug-in allows calcium measurement and FRET analysis. FRET analysis uses
the three-filter method and allows calibration of Ca2+ concentration. The Gordon
method that uses three filter sets allows calculation of FRET efficiency.
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B
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B
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D
E
After deconvolution
EDF: Extended Depth of Focus
Object Classifier
Extended Depth of Focus (EDF) is an additional software plug-in for
NIS-Elements. Thanks to the EDF function, images that have been
captured in a different Z-axis can be combined to create an all-infocus image. Also, it is possible to create stereovision image & 3D
surface image for a virtual 3D image.
Extracted measurement objects can be classified according to
shape, brightness, size and specified characteristics. Measuring and
counting by each class can be conducted easily.
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C
D
Object Tracking
Focused image created from a sequence of Z-stack images
By tracking an object captured by 2D acquisition, speed and distance of
its movement can be measured. Exporting acquired data is also possible.
Database
NIS-Elements has a powerful image database module that
supports image and meta data. Various databases & tables
can easily be created and images can be saved to the
database via one simple mouse-click. Filtering, sorting and
multiple grouping are also available according to the
database field given for each image.
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System Configuration Examples
3D (XYt), 4D (XYZt) Time-Lapse Imaging System
NIS-Elements
software
Cooled CCD
camera
By controlling the shutter attached to a
microscope, long-term time-lapse
observation is possible. As well as
conventional time-lapse acquisition, HighSpeed RAM capturing is possible. By
controlling the Z focus of a microscope, 4D
time-lapse acquisition is also possible,
depending on the thickness (Z-axis
direction) of the specimen.
5D (XYZλt) Imaging System
Shutter
Motorized
barrier
filter wheel
Mercury/
Xenon lamphouse
Motorized inverted
microscope Ti-E
Motorized
excitation
filter wheel
Data analysis
equipment
NIS-Elements
software
Cooled CCD camera
Mercury/
Xenon lamphouse
Motorized inverted microscope
Ti-E epi-fluorescence set
4D (XYZλ) Multicolor Imaging System
NIS-Elements
software
Motorized
barrier
filter wheel
Motorized
excitation
filter wheel
6D (XYZλt Multipoint) Imaging System
Mercury/
Xenon lamphouse
Shutter
NIS-Elements
software
Data analysis
equipment
Industrial System
NIS-Elements
software
By controlling the Z focus of a microscope,
images of the same viewfield with different
focus planes are automatically captured
with the EDF tool to create an all-in-focus
image in the specimen’s depth direction.
Cooled
CCD camera
Motorized XY stage
Motorized inverted microscope
Ti-E epi-fluorescence set
Digital camera
IN
By controlling the motorized microscope, it is possible to
change the focus plane (Z focus) and the excitation and
absorption lights. The experiment program can be easily
set up by selecting the necessary settings without using
the special macro.
Moreover, handling of the acquired image data is made
easy. Various processes also facilitate analysis and
visualization after image acquisition.
Cooled CCD
camera
Motorized inverted
microscope Ti-E
epi-fluorescence set
Data analysis
equipment (PC)
OUT
0
100
By controlling the fluorescence filter wheel,
excitation and absorption lights can be
changed to observe a specimen.
Data analysis
equipment
100
0
Joystick unit
Industrial microscope
LV150A
Data analysis
equipment
Z-focus module
10
Controller
By controlling the motorized microscope and stage,
simultaneous multipoint time lapse and acquisition of
Z-axis information of each of these points is possible.
For example, when imaging multiple XY and Z locations,
wavelength and time can also be acquired in a single
experiment.
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3
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NIS-Elements Supported Devices
Features
Window style
Camera control
Microscope control
Nikon made peripheral device control
Non-Nikon peripheral device control
Live image capture
Time-lapse image capturing (T)
Z-series image capturing (Z)
Multichannel image capturing (λ)
Multipoint image capturing (P)
Multidimensional image capturing
RAM capture
AVI live-stream capture
Objective calibration
Capturing data savings (Meta-data)
Image filtering
Binary
LUT (look up table)
Histogram
Manual measurement
Auto measurement
Intensity line profile
Time (intensity) measurement
3D measurement
Volume measurement
Database
Macro
Advanced interpreter
Report generator
Live compare
ND volume view
EDF
3D surface view
Ratio view
Nikon original deconvolution
AQ blind deconvolution
2D real time deconvolution
Object classifier
Object tracking
FRET & Calcium
Metalogical analysis
AR
MDI
(Multiple
Document
Interface)
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BR
MDI
(Multiple
Document
Interface)
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Nikon Cameras
D
SDI
(Single
Document
Interface)
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A1/C1 Confocal
Digital Sight Series
(1st, 2nd Generation)
DS-1QM*
DQC-FS
DXM1200 Series*
Third-party Cameras
Roper Scientific
QuantEM
CoolSNAP Series
Andor Technology
Luca S, Luca R
iXON+ 987, 888, 885
QImaging
Retiga 2000R - Mono/Color
Retiga SRV + RGB-HM-S Slide
SONY
DFW-X710, SX910
PixeLINK
PL-A662 - Color
Vosskuhler*
1300B
1300QB
1300F
Hamamatsu
ImagEM C9100-13
ORCA 9100-12
ORCA (DCAM)
C9100-02
Imaging Source
Imaging Source Converter DFG/1394
Matrox*
Matrox Meteor II/Multi-Channel
(only PAL)
JVC
JVC KY-F75
TWAIN Device*
Nikon Microscope Devices
Inverted Microscope Ti, TE2000 Series
Upright Microscope 90i, 80i
Multizoom Microscope AZ100
Industrial Microscope LV Series
Measuring Microscope MM-400/800
Fiber Illuminator Intensilight
Nikon Remote Z Focus Controller
Third-party Devices
Prior Scientific
ProScan II (H30)
Prior PCI
ProScan (H29)
OptiScan II, OptiScan
NZ100, 200, 500 nanoStageZ
Lumen Pro
Ludl Electronic Products
MAC5000
Märzhäuser Wetzlar
TANGO Desktop, Tango PCI
LSTEP, ECO-STEP, MCL2, MCL3
Vincent Associates (Uniblitz)
VMM-D3 (only via TE2000)
VCM-D1
Sutter Instrument
Lambda 10-2, 10-3, SC, 10-B
Physical Instrument
PI E-662, 665 (RS232)
Optical Insights
Dual View
EXFO
EXFO XCite120
ASI (Applied Scientific Instrumentation)
MS-2000
FW-1000
SC-2000
*Only compatible with Windows XP
Supported Operation System
Windows Vista Business (x64) SP1
Windows Vista Business SP1 (32-bit Version)
Windows XP Professional SP2 (32-bit Version)
NIS-Elements is compatible with all common file formats, such as JP2,
JPG, TIFF, BMP, GIF, PNG, ND2, JFF, JTF, AVI, ICS/IDS. ND2 is a special
format for NIS-Elements. ND2 allows storing sequences of images
acquired during nD experiments. It contains information about the
hardware settings and the experiment conditions and settings.
○: Full function △: Limited function —: Not available ●/▲ : Option
* Monitor images are simulated.
Company names and product names appearing in this brochure are their registered trademarks or trademarks.
Specifications and equipment are subject to change without any notice or obligation on
the part of the manufacturer. September 2008 ow©2006-8 NIKON CORPORATION
WARNING
TO ENSURE CORRECT USAGE, READ THE CORRESPONDING
MANUALS CAREFULLY BEFORE USING YOUR EQUIPMENT.
NIKON CORPORATION
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phone: +81-3-3773-8973 fax: +81-3-3773-8986
http://www.nikon.com/products/instruments/
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phone: +1-631-547-8500; +1-800-52-NIKON (within the U.S.A. only)
fax: +1-631-547-0306
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phone: +31-20-44-96-222 fax: +31-20-44-96-298
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MALAYSIA phone: +60-3-7809-3688 fax: +60-3-7809-3633
NIKON GMBH AUSTRIA
AUSTRIA phone: +43-1-972-6111-0 fax: +43-1-972-6111-40
NIKON INSTRUMENTS KOREA CO., LTD.
KOREA phone: +82-2-2186-8410 fax: +82-2-555-4415
NIKON CANADA INC.
CANADA phone: +1-905-602-9676 fax: +1-905-602-9953
NIKON FRANCE S.A.S.
FRANCE phone: +33-1-4516-45-16 fax: +33-1-4516-45-55
NIKON BELUX
BELGIUM phone: +32-2-705-56-65 fax: +32-2-726-66-45
NIKON GMBH
GERMANY phone: +49-211-941-42-20 fax: +49-211-941-43-22
NIKON INSTRUMENTS S.p.A.
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NIKON AG
SWITZERLAND phone: +41-43-277-28-67 fax: +41-43-277-28-61
Printed in Japan (0809-05)T
Code No. 2CE-MRPH-5
En
This brochure is printed on recycled paper made from 40% used material.

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