Applications & Technology

Provided here is an overview of the various applications supported by the Nikon BioImaging Lab, detailing imaging, analysis, and other tools we have at our disposal. Click to jump to a specific application, or scroll down to start exploring.

The information on these pages applies to the Nikon BioImaging Lab in Leiden, The Netherlands. There are also laboratories in Shonan, Japan and Cambridge, Massachusetts, USA. For more information, please contact the facility nearest to your location.

High Content Imaging and Analysis

Technology: LIPSI,, cell culturing services

High content imaging is about imaging more – more detection channels, more time points, more data. It’s no wonder that high content imaging and analysis is a powerful tool for so many applications, such as phenotypic screening in drug discovery research. However, the greatest strength of high content imaging – the volume of rich data created – can also be its greatest drawback, creating critical bottlenecks in experiment design, data storage, and image analysis. At the Nikon BioImaging Lab, our high content imaging services are centered around the LIPSI, a stable yet flexible platform for long-term live-cell high content that addresses common process bottlenecks to provide 24/7 operational efficiency.

High content imaging with LIPSI is great for applications ranging from cell health monitoring, to toxicology studies, and much more. For fast imaging thicker samples, LIPSI system, equipped with a set of long-range objectives, features Crest X-Light Series spinning disk confocal system for acquiring data deep in samples such as spheroids, organoids, organ-on-a-chip, and tissue. This system also features our deep learning software modules, which can be trained to perform a number of different analysis tasks, such as segmentation, and can be integrated into an automated imaging and analysis pipeline. Cell culturing services are also available.

3D Imaging

Technology: LIPSI, N-SIM S, AX / AX R, ECLIPSE Ti Series

Cell biology and other fields have long relied on in vitro imaging of a single layer of cultured cells adhering to a flat surface, but the limitations of such model systems are being increasingly recognized, and more physiologically-relevant models are gaining in popularity, including spheroids, organoids, organ-on-a-chip, and similar systems. While these systems provide better models of organismal biology, they have non-trivial thickness and 3D structure, which limits the application of routine 2D widefield imaging approaches.

Our LIPSI system features Crest X-Light Series spinning disk confocal system for fast deep imaging tens of micrometers or more into the sample.

AX series of confocal improves on perfection with unprecedented 3D resolution where best image quality is at reach. Powered by Ai, the confocal imaging system facilitates everyone's experiment from settings to analysis providing the finest customer ownership. AX R offers as well high speed capabilities thanks to high quality resonant scanning.

N-SIM S microscope is supporting 3D multi-color imaging of fixed samples and simultaneous live-cell multi-color imaging of two colors; the resolution is improved up to two times in all directions (X, Y, Z).

Our ECLIPSE Ti2-E inverted microscope is also equipped for 3D widefield imaging, featuring integrated deconvolution software for achieving optical sectioning in samples to approximately 20 micrometers thick. While 3D imaging by widefield deconvolution doesn’t provide the instantaneous 3D sectioning of a confocal instrument, it is fast and often the superior choice for low-signal samples. We understand the nuances that inform proper choice of 3D imaging technique, and are here to make sure you are successful.

Z-stack of a kidney organoid acquired using a Nikon A1R HD25 confocal system.

Red: Actin cytoskeleton (filamentous-actin)
Blue: Nuclei (DNA)

Fluorescence Imaging

Technology: LIPSI, N-SIM S, AX / AX R, BioStudio-T, ECLIPSE Ti2-E

Fluorescence microscopy is widely considered to be one of the most sensitive imaging methods for detecting a given molecular target with high specificity. Fixed samples are generally labeled with dye-conjugated antibodies using standard immunohistochemistry/immunofluorescence techniques. Live samples can be made to genetically express a fluorescent protein fused to a target protein of interest or stained with membrane-permeable organic dyes.

Fluorescence underpins a number of important imaging methods providing a convenient mechanism for multichannel imaging via the labeling of different targets with spectrally-distinct fluorophores. All of our systems are built to perform fluorescence imaging, however there are many factors that must be considered to do so successfully. At the Nikon BioImaging Lab, we have an intimate understanding of concerns related to phototoxicity, sample preparation (including fluorophore selection), and other such critical factors that help determine the success of a fluorescence-based experiment.

Our imaging system are also capable of performing targeted FRAP and photostimulation experiments, FRET studies, and advanced 3D confocal and super-resolution imaging. We stand ready with the expertise to craft successful imaging, having a deep knowledge of fluorophores, microscope settings, mounting media, and related concerns.

Mouse hippocampal neuron. Green: GFP (dendrites), Red: PSD-95-TagRFP (postsynaptic marker). Image acquired using a Nikon CFI SR HP Apochromat TIRF 100XC Oil objective and courtesy of: Drs. Yutaro Kashiwagi and Shigeo Okabe, Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo.

High-Resolution Imaging

Technology: N-SIM S, AX / AX R, ECLIPSE Ti2-E

It’s easy to find a microscope providing high magnification, but it takes much more than magnification alone to acquire quality high-resolution images. Our AX / AX R confocal system provides both optical sectioning – the ability to resolve a distinct 2D section in a 3D sample – and high-resolution imaging of sample features in that 2D section. To maximize the resolution of our confocal instrument, we have the NIS-ER extended-resolution software module for deconvolution of AX R data, which includes detailed point-spread function (PSF) models for Nikon’s market-leading objective lenses.

On top of this, Nikon BioImaging Lab is operating N-SIM S super-resolution system; it utilizes a unique high-speed structured illumination to achieve acquisition speeds of up to 15 fps, enabling fast biological processes to be captured at twice the spatial resolution of conventional light microscopes (~115nm in X, Y and ~269nm in Z). The N-SIM S system is combined with A1-R confocal microscope system creating a single versatile platform for multi-scale imaging.

The ECLIPSE Ti2-E inverted microscope is also capable of high-resolution multi-dimensional imaging – able to acquire data in 3D, over time, and in multiple color channels similar to the AX R – and includes deconvolution software for maximizing resolution and optical sectioning.

It’s not just the microscope that goes into making high resolution images, equally important is proper sample preparation. If, for example, your sample is mounted in a medium with the wrong refractive index, optical resolution will suffer significantly, especially in the Z direction. At the Nikon BioImaging Lab we have you covered on both fronts, with expertise in both high-resolution microscopy and sample preparation.

Cochlear cilia XY and XZ views before (left) and after (right) deconvolution using the A1-ER enhanced resolution module. Image data acquired using a Nikon A1R with a pinhole diameter of 1 Airy Unit.

Label-free Imaging

Technology: LIPSI, BioStudio-T, BioStudio-mini, Ti2-E Inverted Microscope,

While fluorescence imaging might be one of the most popular contrasting technique for optical microscopy, it is also one of the most invasive. Fluorophores are prone to photobleaching, limiting their useful lifetime, and resulting in the need for greater and greater illumination intensity to excite a similar amount of emission as the experiment progresses. This difficulty is compounded by the phototoxic response of live cells to high intensity illumination. Assays using sensitive cell types, such as stem cells, may not be completely compatible with fluorescence imaging of the desired target.

Cell health concerns are helping to fuel the renewed popularity of label-free imaging techniques, which help avoid both the need for high intensity illumination as well as perturbation of the system by the labeling process.

Artificial intelligence-based machine learning and deep learning analysis techniques are also helping to enable this trend. For example, the module (one of several deep learning software modules) automates the identification of key cell features from differential interference contrast (DIC) data, such as the simulated DAPI staining in the figure here. All of our systems support label-free imaging, with available techniques including new volume contrast, phase contrast, differential interference contrast (DIC), darkfield, and brightfield. Contact us today to see if label-free imaging will work for you.


照片来源:北海道大学电子科学研究所技术学院的Kentaro Kobayashi博士

Cell Screening

Technology: LIPSI, AX / AX R Confocal, BioStudio-T

Stem cells are essential tools in regenerative medicine and allied fields, however they can be notoriously difficult to culture and maintain in the undifferentiated state due to their high environmental sensitivity. To address the challenges of culturing stem cells (and other difficult cell types), we operate a Nikon LIPSI system – a microscope system enclosed in an incubator built from the ground up to monitor sensitive cell cultures over an extended period. The system features automatic image capture, ultra-precise vessel exchange (space for up to 20 well-plates in two containers), and AI-based deep learning software tools for various analyses, such as automatic stem cell colony identification and counting.

The BioStudio-T is a compact single-vessel microscope imaging system that fits within an existing incubator. Unlike other microscopes, the sample is held stationary while the objective lens is scanned, reducing disturbance to the sample.

The LIPSI provides many of the same features for cell screening as the BioStudio-T, and may prove preferable for certain use cases, such as deep imaging, where the integrated Crest X-Light Series spinning disk confocal system allows users to image tens of micrometers into live samples with clarity. And it’s not just imaging, we’re ready to help you develop a complete imaging experiment, from facilitation of the cell culture through analysis of the data and process refinement.



High Throughput

Technology: LIPSI, AX R Confocal, ECLIPSE Ti2-E

Where high content imaging and analysis techniques are focused on acquiring and sifting through detailed multivariate data, high throughput is more focused on data volume, even if the dimensionality of that data is low. To be clear though, this doesn’t mean that high content imaging and analysis can’t be performed in a high throughput manner.

The LIPSI and ECLIPSE Ti2-E microscope feature a large 25 mm field of view (FOV) through the camera port, providing approximately twice the imaging area compared to competing microscope systems. Along with our large format cameras and the AX R confocal system, which are able to match the 25 mm FOV, these systems provide very high throughput. Throughput isn’t just determined by imaging area though, but also by acquisition rate. The Ti2-E inverted microscope features fast triggered acquisition, where a firing signal from the camera directly triggers the functions of system devices, bypassing slower software-based controls. The AX R confocal system has a fast resonant-scanning option, allowing for full-frame imaging at 15 frames per second (2048 x 1024). Along with our Denoise.AI deep learning-based denoising software module, you can achieve real-time imaging quality similar to a slow-scanning system.

Multi-point and large image stitching are straightforward to implement in your acquisition workflow in our NIS-Elements software with all the systems described here, making for easy whole-well, whole-slide, whole-vessel imaging.

Mouse embryo

Haematoxylin and eosin staining
CFI Plan Apochromat Lambda 10X
Large image stitch without boundary artifacts
Autofluorescence image