Light-sheet microscopy is an imaging approach that offers unique advantages for a diverse range of neuroscience applications. Unlike point-scanning techniques such as confocal and two-photon microscopy, light-sheet microscopes illuminate an entire plane of tissue, while imaging this plane onto a camera. One such application is in large-scale neural recordings. The strength of light-sheet microscopy for systems neuroscience is that it gives researchers the ability to record from many cells at the same time. Indeed, measurements of neural activity across the whole brain, or at least a very large fraction of it, have been something of a holy grail for neuroscientists. Large-scale optical recording methods such as light-sheet imaging are providing these types of data.

Light-sheet functional imaging at the scale of the entire brain is subject to the fundamental tradeoff between temporal and spatial sampling. Although lateral resolution (i.e., resolution within the image plane) is usually fairly high, in most light sheet microscopes, axial resolution (i.e., resolution perpendicular to the image plane) is often at least partially constrained by axial sampling as a result of the need to minimize the number of image planes covering the sample volume. Our QLS-scope is the only microscope in the market that can provide evenly high spatial and axial resolution for the whole brain.


For decades, pathologists have used hematoxylin and eosin staining or other assistive techniques such as immuno-histochemistry or in situ hybridization to examine and stage tumor sections with bright-field or fluorescence microscopy. The results of these pathological examinations are used to diagnose diseases, predict patient prognoses, and decide treatment plans. However, the assessment of tumor sections with conventional analog microscopes are labor and time intensive processes that do not provide complete information. Histopathological examination is commonly performed on tissue samples that have been fixed and then thinly sectioned, stained, and mounted on glass slides. Usually, only a small fraction of the entire tumor is sectioned and examined under microscopy. This creates an information gap between the limited 2D images assessed and the original state of the 3D tumor, which could be vital for the assessment of diseases that are challenging to diagnose and grade, with potentially significant consequences for patients. Solid cancers exhibit complex 3D micro-environments consisting of heterogeneous populations of cells of various sizes, different genotypes, and distinct phenotypic characteristics.  This intratumoral heterogeneity is central to the natural selection that drives the processes of carcinogenesis, metastasis and acquired resistance to therapeutic interventions. For example, epithelial-to-mesenchymal transition (EMT) and angio-genesis are processes involved in creating heterogeneous tumor landscapes and unique 3D masses.  The ability to characterize these intratumoral features in patient specimens would significantly help in improving the diagnosis and grading of cancers and for guiding treatment decisions. Light-sheet microscopy is an ideal tool for histopathology since it enables object visualization in three dimensions and enables both rapid and deep volumetric imaging of whole tissues.


Cardiovascular diseases are the most prominent global health threats. For optimal treatment, myocardial biopsies are an indispensable requirement. Current analysis includes histological and biochemical assays with particular limits. Light sheet fluorescence microscopy (LSFM) makes possible visualize the 3D vasculatory architecture in the heart after experimental myocardial infarction (MI) in human cardiac biopsies with simultaneously imaging of various immunological infiltrates for disease investigation.

In the other hand, real-time 3-dimensional (3-D) imaging of tissue development and regeneration remains an optical challenge. Conventional optical microscopes are limited by low tissue penetration and small working distance, which are prohibitive to long-term live imaging that requires rapid data acquisition to minimize photobleaching and phototoxicity to the specimens. In addition, samples must be mechanically sectioned, thereby distorting intrinsic tissue integrity and subsequently resulting in undersampling after 3-D reconstruction. While PET, μCT, MRI and bioluminescence imaging are capable of capturing 3-D imaging from live, the spatial resolution of these techniques is inadequate to capture organ morphogenesis in small-animal models. For these reasons, light-sheet fluorescence microscopy (LSFM) has revolutionized multiscale imaging, allowing visualization of samples ranging from live zebrafish embryos (~ 0.4 × 0.5 × 0.6 mm3) to adult mouse hearts (~8 × 8 × 10 mm3) with high-spatiotemporal resolution and minimal photobleaching and phototoxicity.

Developmental biology

Within only a few short years, light sheet microscopy has contributed substantially to the emerging field of real-time developmental biology. Low photo-toxicity and high-speed multiview acquisition have made selective plane illumination microscopy (SPIM) a popular choice for studies of organ morphogenesis and function in zebrafish, Drosophila, and other model organisms. In particular, developmental biology can benefit from the ability to watch developmental events occur in real time in an entire embryo, thereby advancing our understanding on how cells form tissues and organs. However, it presents a new challenge to our existing data and image processing tools.

While zebrafish, Drosophila, and mouse embryos are perhaps more conventionally recognized model organisms, light-sheet microscopy has also proven quite useful for the study of other model organisms that previously have not been closely examined, largely due to the difficulty of imaging them by using standard confocal methods. The arthropod crustacean Parhyalehas a Swiss army knife–like collection of limbs, each developing from specific regions of the embryo, and has proven to be both optically accessible and highly tolerant to light-sheet imaging, yielding interesting insights into limb development. Additionally, chick and quail embryos are of interest to developmental biologists, as they develop morphologically similarly to human embryos, can be genetically modified, and (when used with an inverted light-sheet setup) provide stunning views of neurulation and primitive-streak formation.

Infectious diseases

With every breath, lungs are exposed to potentially harmful air-borne pollutants and pathogens that may damage the airways. To cope with repetitive challenges and to rapidly replace lost or impaired cells, the pulmonary epithelium requires a high regenerative potential. To gain insights into regenerative processes not only at a cellular level, but also at an organ-wide scale, it is necessary to visualize the dynamics of distinct cell populations during lung regeneration at a three-dimensional (3D) spatial resolution. Acquisition of 3D data is of great importance, in particular for highly specialized organs with a complex architecture and varying regional (micro) environments. Only 3D imaging allows reliable detection of local, eventually rare events in large volumes and a better understanding of topological cellular interactions. Light sheet microscopy and the most recent clearing methods, make the perfect combination for 3D imaging of whole lung animal models.

Plants biotechnology

Plants have a diverse and flexible architecture based upon relatively simple repetitive units. However, in contrast to animals, most organogenesis occurs post-embryonically and in two confined areas called meristems, which are located in the apical (shoot) and basal (root) ends of the plant. This peculiar mode of development has led to interest in studying the dynamics of organ formation and growth in a living organism. Imaging the development of roots is particularly problematic since its growth is influenced by gravity. In addition, since plants scatter and absorb light remarkably well, they are exposed to intense light to ensure proper illumination and detection of signals from the entire volume. The use of very high light intensities results in heating and photo-toxicity problems, which induce the malfunction and death of a specimen. Finally, if the experimental measurements obtained are to represent normal development, there is a need to keep the sample under physiologically sustainable conditions while maintaining a high image acquisition rate. Our QLS-scope light sheet microscope is the ideal imaging tool to monitor the plant growth in three dimensions while keeping it in physiological conditions.