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. 2 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 3 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. 2 1 3 0 sec. 4 15 sec. 30 sec. Volume rendering Orthogonal image Tiled image 5 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). 6 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. 7 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. A B A B C 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. E 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. 8 9 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. 2 1 3 2 1 3 2 1 3 11 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) ○ ○ ○ ● ○ ○ ○ ○ ○ ● Up to 6D ○ ○ ○ ○ ○ ○ ○ ○ ○ ○ ○ ○ ● ○ ● ○ ○ ○ ○ ○ ● ● ○ ● ● ● ● ● ● — BR MDI (Multiple Document Interface) ○ ○ ○ ● ○ ○ ○ ○ ○ ● Up to 4D — ○ ○ ○ △ △ ○ ○ ○ ○ ○ ● ▲ — ● △ ● ○ ● △ ● ● — — — — — — — — Nikon Cameras D SDI (Single Document Interface) ○ ○ ○ ● ○ △ ○ — ○ — — ○ ○ ○ △ ▲ ○ ○ ○ ● ○ — ▲ — ● △ ● ○ ● △ ● ● — — — — — — — ● 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 6-3, Nishiohi 1-chome, Shinagawa-ku, Tokyo 140-8601, Japan phone: +81-3-3773-8973 fax: +81-3-3773-8986 http://www.nikon.com/products/instruments/ NIKON INSTRUMENTS INC. 1300 Walt Whitman Road, Melville, N.Y. 11747-3064, U.S.A. phone: +1-631-547-8500; +1-800-52-NIKON (within the U.S.A. only) fax: +1-631-547-0306 http://www.nikoninstruments.com/ NIKON INSTRUMENTS EUROPE B.V. Laan van Kronenburg 2, 1183 AS Amstelveen, The Netherlands phone: +31-20-44-96-222 fax: +31-20-44-96-298 http://www.nikoninstruments.eu/ NIKON INSTRUMENTS (SHANGHAI) CO., LTD. CHINA phone: +86-21-5836-0050 fax: +86-21-5836-0030 (Beijing branch) phone: +86-10-5869-2255 fax: +86-10-5869-2277 (Guangzhou branch) phone: +86-20-3882-0552 fax: +86-20-3882-0580 NIKON SINGAPORE PTE LTD SINGAPORE phone: +65-6559-3618 fax: +65-6559-3668 NIKON UK LTD. UNITED KINGDOM phone: +44-208-247-1717 fax: +44-208-541-4584 NIKON MALAYSIA SDN. BHD. 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. ITALY phone: +39-055-300-96-01 fax: +39-055-30-09-93 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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