Cookies on the Nikon Instruments website
We use cookies to ensure we give you the best experience on our website. If you continue we'll assume
that you are happy to receive all cookies on the Nikon Instruments website.
Find out more about our cookie policy


Nikon Instruments Europe B.V. | Europe & Africa

Skip to main content

Microscope Imaging Software

Request a Quote

The ideal microscope imaging software for easy capture, processing, reporting and storage.

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.

Key Features

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

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.

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.


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.

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.


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’.

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.

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.

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.

Back to top