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YOU ARE HERE : > Product > Softwares > Nikon Software > NIS-Elements D Microscope Imaging Software

NIS-Elements D Microscope Imaging Software

Product Code : NIS-Elements D

Brand : Nikon

NIS-Elements D utilizes a single window graphical user interface tailored for facilitating image capture, object measurement and counting, databasing and report generation. Menu options have been streamlined, making this the most intuitive and easy-to-use microscopy software package on the market. The combination of integrated automated intelligence, streamlined workflow, attention to detail and creative design makes NIS-Elements Documentation the perfect package for clinical and industrial applications such as particle analysis, defect analysis and fiber & textile material analysis.

Key modules in the package include an optional database capability allowing one-click image acquisition and transfer from a camera to a user-defined database. A report generator allows users to create report templates for PDF-based reports. The product also includes sophisticated large image stitching capabilities, enabling the capture of ultra-high resolution images with a motorized stage. Optional plug-ins are available, such as the Extended Depth of Focus (EDF) module, which creates an all-in-focus image from a series of Z-axis images.

More About

NIS-Elements D Microscope Imaging Software

General Tools

The NIS-Elements Documentation package supplies a base of broad tools that address common imaging needs. Learning and moving though the package is made easy by customizable window layouts, simple workflow for switching between controls, dialogs and live and saved images. NIS-Elements Documentation is compatible with all common file formats and incorporates nondestructive archiving of single images and image sequences, annotations, calibrations and other image data.


Image Format

Image Format

NIS-Elements incorporates an advanced multi-layered document structure using lossless JPEG 2000 image format. This image documentation structure makes it possible to achieve nondestructive archiving of image data including annotation (arrows, lines, and text notes), measurement data, binary data for storing results of threshold areas and meta-data information for recording acquisition and device conditions at the time of image acquisition. NIS-Elements is also compatible with all common file formats (TIFF, JPG, BMP, AVI, and ICS/IDS).

To save image sequences with lossless image quality, NIS-Elements has designated the ND2 format as its special format. ND2 allows storing sequences of images such as a Z-stack, multiple stage positions and images over time. All sequential information for the image series is located on the toolbar of the image window. This feature makes previewing and scrolling though image sequences extremely easy and intuitive.

In addition, ND2 contains information about the hardware settings and the acquisition conditions.


Layout Management

NIS-Elements offers the user the choice of two built-in layouts in which to operate the software. The ‘Docked Controls’ mode allows hardware and application dialogs to be pinned on screen together with image windows (shown below, circled in red). In addition, the ‘Full Screen’ mode displays only the image of interest plus selectable controls. Layouts of all windows and docked controls can be freely customized and added by the user and saved. Switching between layouts is achieved by a single mouse click.

Layout Management

Autosave Folder (Filmstrip View)

Within the layout of NIS-Elements, an ‘Auto Save Folder’ is also available. This useful interactive display tiles images from a selectable directory. Images from any file or database on the system are easily accessed and brought into the active window view.

Autosave Folder


Simple image capture and preparation has never been more flexible using NIS-Elements Documentation. This comprehensive solution includes intuitive camera controls, microscope and device controls, annotation tools and saving and retrieving functions from an uncomplicated and fully-searchable database. The report generator collects images and associated data, auto-updating as necessary, and saves or exports to a printer or PDF file.


Image Preparation: Annotation and Enhancement

One of the key modules in NIS-Elements is the advanced but easy-to-use database functionality.  You can save an image directly into the database with one mouse click and filtering, sorting and multiple grouping can be easily performed by drag and drop. Detail, thumbnail, icon and grid views are available on both the database image and the images on the file system.


Database Option

One of the key modules in NIS-Elements is the advanced but easy-to-use database functionality.  You can save an image directly into the database with one mouse click and filtering, sorting and multiple grouping can be easily performed by drag and drop. Detail, thumbnail, icon and grid views are available on both the database image and the images on the file system.

Database Option

Report Generation

Report Generation

Report generation is a key feature of the database. Report templates can be created with customized text, graphs, and image files such as company logos or other picture files (shown below). The ‘Report Generator’ can also automatically pull information stored with the image. Modifiable text fields will auto update with the image information that is specified in the table of the database. Reports can be saved, directly printed and/or converted to a PDF file.


Macros and API (Advanced Interpreter) Option

Flexibility in custom tailoring the software for specific applications is possible through simple built-in macro recording and the Advanced Macro Builder (API (advanced interpreter)). The optional API allows for more complex programming such as conditional statements, looping, arrays, operators and local and global variables.


Acquisition Tools

NIS-Elements Documentation offers the user the choice to add one dimension for image capture, Z-motor control for a Z-series, stage control for multiple stage positions (ideal for large image stitching) or a time-lapse to observe any changes over time. One can be utilized at a time, but all three additional dimensions are available.



Images at different Z-axis planes can be captured with a motorized Z-Focus control.

Two methods of capture in the Z-axis – ‘Absolute Positioning’ and ‘Relative Positioning’ – are available. The ‘Relative Positioning’ method has ‘Symmetric’ and ‘Asymmetric’ variations. With Symmetric Z-capture, the number of Z-steps is exactly the same around the home position. Alternatively, with Asymmetric Z-capture, variations in Z-steps around the home position can be configured.



With a motorized stage installed, it is possible to automate the capture of images at multiple points in XY (and optionally Z) across the sample.

Multipoint Acquisition

Time Lapse

The ‘Time Sequence Acquisition’ allows for simple configuration of data collection over time. The only parameters that must be entered for configuration are ‘Interval’ and ‘Duration’.

Time Lapse

Live Compare Option

The ‘Live Compare’ module is ideal for comparing a live image with a stored image for applications such as defect analysis, Go-No-Go assessment and more.

Viewing of a stored image and a live image can be displayed in various formats. 

Pictured below is an example of a stored image with a live image beneath to compare color variation on a silicon wafer side.

Live Compare

Automated Imaging

High-resolution images can be created with the precision of NIS-Elements Documentation large image stitching feature. In addition, an Extended Depth of Focus (EDF) option is available to allow images from different Z-axes to be combined into one focused frame and viewed as a virtual 3D or stereovision image.


Large Image Stitching

NIS-Elements includes remarkably accurate large image stitching capabilities, allowing the capture of ultrahigh resolution images. Capture and stitching can be completed with or without an automated stage. Large image stitching is a useful tool for the common occasion when the sample or area of interest is larger than the field of view of the camera. If it is not optimal to decrease the magnification, a large image stitch is a robust solution.

Large Image Stitching

EDF (Extended Depth of Focus) Option

EDF allows images that have been captured in a different Z-axis to be combined, creating an single all-in-focus image. Once the all-in-focus image has been created, it can be viewed and rotated as a virtual 3D image as well as displayed as a stereovision image. EDF also has an option to re-align images acquired through stereomicroscopes, correcting for parallax shift. Optional plug-in modules are available that allow the creation of an all-in-focus image from a series of Z-axis image stacks providing 3D modeling capability and a multi-dimensional image viewer. The EDF module generates an image that incorporates the focused portions of each image from a Z-series of images. In addition, Real-time EDF is also available. The module saves time as it builds the focused image as the image is acquired.

Extended Depth of Focus Option



Several measurement choices are available and may be included as annotations on the image and data is displayed in a spreadsheet view. Interactive cross referencing, and live image measurements are also available and simple to perform. A profile tool plots measurement statistics and other criteria onto an interactive graph that can be exported into various file formats.

NIS-Elements incorporates many choices for measurements and analysis. Each is flexible and easy to use. Several measurements are available: area, length, counts, taxonomy, radius, semiaxes, and angle.

Measurement data is shown with annotations on the image and in a spreadsheet view. Interactive cross referencing is possible between the measurements on the images and in the data from the spreadsheet view. Measurements can also be created on a live image, as shown below. Standard lengths can be displayed on a live image to test for fit or a feature and exporting the data to Excel, HTML or text file is also possible.


A profile tool is also available for plotting intensity, brightness or density into an interactive graph. All output measurement statistics, histograms, and profile graphs can be exported to Excel, HTML, or to a text file.


Operating Environment

All PC environments should meet the following minimum requirements:

CPU 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 & Cameras
Microscopes 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 & Devices
  • 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

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