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YOU ARE HERE : > Solutions > Software > Nikon Software 2 > NIS-Elements Ar Microscope Imaging Software

NIS-Elements Ar Microscope Imaging Software

Product Code : NIS-Elements

Brand : Nikon

NIS-Elements AR provides a total imaging solution covering image capture, archiving, and analysis. It was developed by Nikon for the most advanced levels of research—giving the user complete control of all microscope and camera functions.

The software is geared to deliver power and maximize workflow. It handles multi-dimensional imaging flawlessly, with support for capture, display, peripheral device control, and data management and analysis of up to six dimensions (X,Y,Z,Lambda(wavelength),T, multipoint). It also offers sophisticated image processing features, such as an extremely powerful deconvolution module, exclusive one-click database capability, and Extended Depth of Focus function.

The system contributes to experiment efficiency with a database building feature developed to handle archiving and searching of large numbers of multi-dimensional image files.

Unified control of the entire imaging system offers significant benefits to users for cutting-edge research, such as live cell imaging.

More About

NIS-Elements Ar Microscope Imaging Software

Live Cell Acquisition

NIS-Elements performs live cell, 6D experiments quickly and flawlessly. It can organize X, Y, Z, Lambda (wavelength) and Time within one integral platform, for easier-than-ever multi-dimensional imaging. Four types of “dimensions” of acquisition – Time, Multipoint, Z-series, Wavelength (Multichannel)— can be selected.


RAM Capturing

RAM capturing enables the recording of sequences displaying very quick acquisitions lasting tens of milliseconds, by using a part of virtual memory to store temporary data of live images.

RAM Capturing

Multi-layer Document Structure

Each document (Image windows) is a three-tiered layer structure, and is therefore ideally suited for analysis. Multiple layer save is available with JPEG2000/ND2/LIM format.

Multi-layer Document Structure

NIS-Elements can work for all common file formats, such as JPEG2000, ND2, TIFF, JFF, JPG, JTF, BMP, LIM, 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.


ND Viewer (Multidimensional image display)

Easy-to-use parameters for multi-dimension image operation are located on the frame of the screen.

ND Viewer


Once a multi-dimensional image is acquired, it can be analyzed via NIS-Elements’ multiple processing functions.


ND Tools

A series of images from timelapse acquisition, or captured Z-stack images, can be easily converted to ND2 format. The converted images can be viewed and processed using features of NIS-Elements multidimensional document.

ND Tools

Image Quantification

NIS-Elements innovative analysis capabilities include object counting, automated measurements, region of intent measurements and time measurements including image ratioing of multi-channel images.


Image Segmentation

Using the RGB or HSI color spaces, NIS-Elements can segment the image and create binary images. Using the binary image, Automatic Measurement records length, area, angle and colorimetry.

Image Segmentation

Automatic Measurement

Using binary objects, NIS-Elements can automatically measure sets of length, area, density and colorimetry parameters. About 30 different object features can be measured.


Interactive Measurement

The measurement is performed by, for example, directly drawing two parallel lines on the screen. Features are available from: taxonomy, counts, length, semiaxes, area, angle or profile and all output statistics and histograms can be exported to MS Excel.

Interactive Measurement


There are five possible interactive profile measurements: free line, two-point line, horizontal line, vertical line, and polyline.



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, HIS values, or RGB values ignoring intensity. The classifier enables data to be saved in separate files.


Time Measurement

Time measurement records the average pixel intensities within defined probes during a time interval and can be performed on live camera signals.


Measurements Across Time

Non-destructive measurements across time can be performed on live camera signals. Time Measurement records the average pixel intensities within defined probes during a time interval. Analysis can be performed pre- or post capture, with assurance that the specimen will live on after acquisition.

Time Measurement

The software also handles:

  • Single, dual, multiple fluorophores
  • Ratiometrics

Advanced Image Processing

NIS-Elements innovative image processing capabilities give users’ further control and functionality in their experiments. Advanced visualization methods, like capturing 3D data sets, 2D/3D data set analysis, and large image stitching can all be performed with relative ease with the software.



NIS-Elements offers a rich spectrum of mathematical morphology functions (clean, erode, dilate, open, close, smooth), morphologic separation functions, linear morphology functions, fill functions (fill holes, close holes), skeleton functions (medial axis, skeletonize, pruning) and other functions (such as: binary invert, convex hull, contour, skeletonize, homotopic marking, zones of influence, etc.).


(original, contour, threshold, zones of influence + source)


Merge Channels

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 a RGB image.

Merge Channels

Image Arithmetic (A+B/A-B/Max/Min)

NIS-Elements’ Image Arithmetic function performs calcuations on the color channels of two images and creates a new image that is a combination of the two.

Image Arithmetic

Large Image Stitching

NIS-Elements includes impressive large image stitching capabilities. Here's how it works: samples are scanned automatically using a motorized XY stage with auto-focus capability and captured images are stitched into one large image. Special algorithms ensure maximum accuracy, resulting in ultra high-resolution images.

Image Stitching

EDF (Extended Depth of Focus)

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-in-focus image. Also, it is possible to create stereovision image & 3D surface image for a virtual 3D image.

2D Deconvolution

Real Time 2D Deconvolution

The real time 2D deconvolution module (from AutoQuant) allows the user to observe live specimens with less out-of-focus blur. It allows faint biological processes to be observed that may otherwise be missed and increases observed signal-to-noise ratio. Available in two- and three-dimensional image stacks.



NIS-Elements makes fluorescence and brightfield photodocumentation easy and intuitive, and offers extensive data management functions. The software’s interface is designed to simplify workflow, and delivers fast image acquisition speeds via direct streaming RAM to record rapid biological events. It provides complete control over Nikon motorized microscopes and other devices with powerful functions like a zoom control linked to calibration.


Selectable Layout Interface

NIS-Elements comes with the built-in layouts “Full Screen” and “Docked Controls.” Layouts of all windows and toolbars can be freely customized by the user and saved. Switching between layouts is achieved by a single mouse click.

Selectable Layout Interface

Acquisition Color Setting

Color modification can be easily set with the LUT (look-up table). Indexed-color pixels are mapped into a selected set of true color values. The histogram, threshold, gamma parameter, and brightness of RGB components are adjustable. Modifications on live image processing can be easily accomplished on the GUI.

Acquisition Color Setting

Data Management

NIS-Elements has a powerful built-in image database. The database supports image and meta-data, allowing users to create report templates or direct printed and PDF based reports. Various databases and tables can easily be created and images can be saved to the database via one simple mouse click.

In addition, filtering, sorting and multiple grouping can all be performed through the GUI's drag and drop functionality. Detail, thumbnail, icon and grid views are available on both the database image and the images on the file system.

Data Management

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.

Image Documentation Structure

Flexibility in tailoring the software for specific applications is possible through simple built-in macro recording and the Advanced Macro Builder.

Advanced Macro Building

Report Generation

Report Generator enables the user to create customized reports containing images, database descriptions, measured data, user texts, and graphics.

PDF format files can be created directly from NIS-Elements.

Report Generation

Easy Access to Image Controls

All vital controls can be accessed by minimal mouse clicks.

Easy Access to Image Controls

Color Adjustment

NIS-Elements is suitable for hue adjustment, independently for each color, transforming the color image to one of the RGB or HSI components.

Color adjustments include:

  • Contrast
  • Background subtraction
  • Component mix
Color Adjustment

Operating Environment

All PC environments should meet the following minimum requirements:


Intel Core 2 Duo or higher


32bit Operating System: 2GB or higher

64bit Operating System: 4GB or higher

Operating System

Windows Vista 32-bit Business Edition (Ar, Br and D supported)

Windows Vista 64-bit Business Edition (C, Ar, Br and D all supported)

Windows 7 32-bit Professional (Ar, Br, and D supported)

Windows 7 64-bit Professional (Ar, Br and D supported)   

Note: F is ONLY supported in Vista Business 32bit (not U3 compatible) and Windows 7 Pro 32bit*Note: NIS-Elements cannot be installed on Windows XP Operating Systems.

Hard Disk

2GB or more required for installation


1280x1024, True Color mode

For optimal volume viewing, video card must be able to support Microsoft’s Direct X (Direct Draw and Texturing) version 9.0C or higher.


Administrator Authorized Users for installing

Administrator Authorized for operating recommended but not required



Nikon Devices & CamerasMicroscopes and Accessories

  • Eclipse Ni-E, Ni-U

  • Eclipse Ci-E

  • Eclipse Ti-E

  • Eclipse TE2000E, TE2000E2

  • Eclipse TE2000-PFS (Perfect Focus System)

  • LiveScan SFC (Swept Field Confocal)

  • Eclipse MA200

  • Eclipse LV150 Series, LV100D, LV100 POL

    • All Nikon motorized components (FMA, Episcopic Illuminator, Nosepiece, etc.)

  • Eclipse i-Series 90i

  • All Nikon motorized components (Focus, XY Stage, ND Filter Unit, Nosepiece, Condenser, Field Diaphragm, etc.)

  • Digital Imaging Heads (DDH-E (motorized) and D-DH-M)

  • Illumination: Intensilight E

  • Prairie Laser Launch with Nikon 8 Channel AOTF I/O Controller (USA only)

  • Photonics Instruments Mosaic and Micropoint (USA only)

  • LU4A Laser Unit

  • Agilent 4 Line Monolithic Laser Module (USA Only)


Cameras and Controllers
  • Digital Sight Cameras:

  • DS-Fi1, DS-5M, DS-5Mc, DS-2Mv, DS-2MBW, DS-2MBWc, DS-1QM, DS-Ri1, DS-Qi, DS-Vi1

  • DQC-FS EMCCD Monochrome Digital Camera

  • Controllers: L3, L2, U1 (32-bit only), U2, U3

Other Cameras & DevicesCameras

  • Photometrics Cameras

    • CoolSnap Series, Cascade Series, PVCAM compatible cameras

    • Only Support Non-LVSD Camera Models

  • Q Imaging Cameras

    • Retiga (models 2000R, SRV+RGB-HM-S Slider, EXi, EXi Blue, EXi-Aqua)

    • Rolera EM-C2, QIClick, QICAM QIC-F-CLR-12

  • Lumenera 1-2CB and 1-3C

  • Hamamatsu ORCA ER Firewire Camera, C9100-12, C9100-13, R2, ORCA-Flash2.8, Orca-Flash4.0, ORCA D2, ImagEM, ImagEM-1K

  • Andor Neo sCMOS, Zyla sCMOS, iXon X3, iXon+ (models 897, 888, 885), iXonEM, iKon-M, Clara, Luca S, Luca R


  • Stages:

    • Prior ProScan, ProScan III, OptScan, ES10ZE

    • Applied Scientific Instrumentation (ASI) MS-2000

    • Ludl MAC 5000 / MAC 6000 Controller

    • Märzhäuser: Tango, LSTEP, ECO-STEP

    • Scientifica XY Linear Stage

  • Filter Wheels:

    • Prior Filter Wheel System

    • Sutter Wheels, Shutters, Controllers: Lambda 10-2, 10-3, 10-B

    • Applied Scientific Instrumentation (ASI) FW-2000

    • Ludl MAC 6000 Controller

  • Wavelength Switching/ Excitation System:

    • Sutter DG 4 / DG 5 (Ultra-High Speed Wavelength Switcher)

    • Nikon LUSU (Laser / Shutter Unit)

    • Lumencor Spectra, SpectraX, Aura

    • 89North Heliophor

  • Shutter Control:

    • Uniblitz Shutter Controller VCM-D1

    • Sutter: Smart Shutter Standalone Controller

    • Applied Scientific Instrumentation (ASI) SC-2000

    • Ludl MAC 6000 Controller

  • Z Motors:

    • Nikon Motorized Z-Focus Accessory (RFA)

    • Prior Z-motor, ES10ZE, NIKRFK

    • Applied Scientific Instrumentation (ASI) MS-2000

    • Physik Instrumente Piezo E-665 (RS232)

    • All Piezo Devices Accepting Voltage

  • Camera Emission Splitters:

    • Optical Insights Dual View, Quad View

  • Illumination:

    • Lumencor Sola

    • Lumen Dynamics X-Cite120, X-Cite LED1 (EXFO)

    • Prior Lumen Pro

    • Sutter Lambda XL

    • CoolLED

  • High Speed Analog Output Boards:

    • National Instruments DAQ Board (NI PCI6503, PCI6519, PCI6711, PCI6713, PCI6731, PCI6733, PCI6220, PCI6221, PCI6221(37pin), PCI6224, PCI6225, PCI6229, PCI6280, PCI6281, PCI6284, PCI6289)

  • Heating Controllers:

    • Linkam TP 95, 94, 93, 92

  • Incubators

    • OKOLab Microscope Incubators

    • Tokai Hit Microscope Incubators


NIS-Elements Ar Microscope Imaging Software

NIS-Elements AR provides a total imaging solution covering image capture, archiv...