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Microscope Imaging Software

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The total microscope imaging software solution covering image capture, archiving, and analysis.

NIS-Elements AR 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.

Key Features

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.

Hardware Triggering

Modern live cell imaging experiments demand optimal system performance, lost seconds can be the difference between failure and discovery.  Most microscope software allows for control of imaging devices, including fast piezo z drives, filter wheels, and more.  However, performance at the advertised device specifications is seldom realized in a real-world setting.  So how does one maximize the overall speed performance of their system? 

Microscope devices are typically controlled using serial communication with the software, which introduces latencies due to checks/callbacks, lack of parallelization, and other factors.  Nikon Instruments offers a comprehensive suite of solutions for maximizing imaging speed via hardware triggering:  a control method using direct I/O voltage-mediated connections to drive system devices.  Signals are managed using a National Instruments data acquisition device (NIDAQ), which has a far more precise timing clock than a PC.

Hardware triggering easily doubles (or more) the image acquisition rate compared to software control for a number of common experimental configurations (Table 1).


  Experiment Duration
Experiment Software Triggering Hardware Triggering
3λ, 60 Z positions 40 sec 18 sec
96 stage positions, 3λ, 10 Z positions 12 min 15 sec 6 min 21 sec
Timelapse: 10 loops, 3λ, 15 Z positions 1 min 38 sec 49 sec
Timelapse: 10 loops, 3λ, 10 Z positions* 1 min 13 sec 10.7 sec

Table 1:  Comparison of experiment durations with typical hardware and experiment parameters.  Hardware triggering displays a significant improvement in overall experiment time.  In these examples, the camera exposure time is longer than the camera readout time for most examples.  *The last row illustrates a comparison when the camera exposure time is the same as its readout time, and the camera can run in overlapped (100% duty cycle) mode. 

Nikon is unique in providing the world’s first completely hardware-triggerable microscope stand, the Eclipse Ti2-E.  We also greatly simplified both the software and hardware setup of devices for triggering with our new NI-BB kit, a central hub providing predefined NIDAQ connections for all your triggered devices.

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.


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.



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


Multi-dimensional image


Orthogonal image


Volume rendering

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.


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.


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.



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.

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 toanother. 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.


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.


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.


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.


Focused image created from a sequence of Z-stack images


Virtual 3D image

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.


Full screen


Docked controls

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.


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.


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.


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


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.


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