Gigapixel fluorescence microscopy with a water immersion microlens array
TL;DR: High throughput gigapixel fluorescence microscopy with a microlens array is demonstrated with a parallelized microscopy system to image samples in micro well plates and fluorescent imaging of tissue samples through coverslips is demonstrated.
Abstract: We demonstrate high throughput gigapixel fluorescence microscopy with a microlens array. We show, for the first time to the best of our knowledge, the use of a parallelized microscopy system to image samples in micro well plates. We image centimeter-scale regions of 384-well micro well plates at 1.72 μm resolution at a raw pixel throughput of 25.4 Mpx/s. Taking into account the fact that about half the well plate area consists of the plastic support region between wells, this corresponds to a sample pixel throughput of 13.2 Mpx/s, more than double that of the commercial state-of-the-art at the time of writing. Fluorescent imaging of tissue samples through coverslips is also demonstrated.
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Patent•
05 Feb 2014TL;DR: In this paper, a plurality of regions of interest are selected on the target at a system control, and the selected plurality is simultaneously imaged to provide an image with the plurality of areas of interest selectively magnified by a microlens array (30) and the regions that are not of interest were rejected by means of a mirrored aperture array, a mask, or selective illumination of the target.
Abstract: Systems and methods are provided for imaging a target as for example a multiwell plate. A plurality of regions of interest are selected on the target at a system control. The selected plurality of regions of interest are simultaneously imaged to provide an image with the plurality of regions of interest selectively magnified by a microlens array (30) and the regions that are not of interest are rejected by means of a mirrored aperture array, a mask, or selective illumination of the regions of interest of the target.
3 citations
Patent•
04 Aug 2016
TL;DR: In this paper, a multifocal spectroscopic measurement device with which it is possible to simultaneously measure a plurality of samples at high sensitivity, with no limitation as to the magnification factor is presented.
Abstract: Provided is a multifocal spectroscopic measurement device with which it is possible to simultaneously measure a plurality of samples at high sensitivity, with no limitation as to the magnification factor. This multifocal spectroscopic measurement device 10 disperses light by introducing into a spectrograph signal light that is emitted from a plurality of prescribed observation areas in a sample S arranged in a sample arrangement part (sample holder 13), the device comprising a plurality of objective lenses (objective focusing parts) 111, a single one of which is provided at each of locations corresponding to optical systems of the plurality of observation areas, and spectrograph input units 151, a single one of which is provided in corresponding fashion to each of the plurality of objective lenses 111, the spectograph input units 151 inputting signal light that has passed through the corresponding objective lenses 111 to a spectrograph 17. Because each of the objective lenses 111 individually observes only a single observation area, the magnification factor can be increased and the numerical aperture NA enlarged. In so doing, the quantity of light collected by the objective lenses 111 in proportion to the quantity of light of all signal light emitted by the sample S in the observation areas is increased, and the measurement accuracy is higher.
2 citations
Patent•
02 May 2019
TL;DR: In this paper, sample dishes for use with microscopes that are simple to mount on a microscope and facilitate easy manipulation of tissue samples disposed thereon during imaging as well as methods of their use.
Abstract: Disclosed herein are sample dishes for use with microscopes that are simple to mount on a microscope and facilitate easy manipulation of tissue samples disposed thereon during imaging as well as methods of their use. A sample dish comprises an optical interface and, optionally, a support member that holds the optical interface. The optical interface of a sample dish is suitably transparent and planar such that a focal plane of a microscope can reside uniformly at or within a surface of a sample during imaging. In certain embodiments, a support member comprises a dish for holding excess fluid. In certain embodiments, a sample dish comprises separation ribs. In certain embodiments, a sample dish comprises one or more manipulation members (e.g., tabs). In certain embodiments, a sample dish is used with an imaging artifact reducing fluid.
1 citations
TL;DR: In this paper, a simple and easy-to-access approach to efficiently sensitize the fluorescence detection to microwell plate was constructed, taking the advantage of higher refractive index of soda lime glass than that of ambitious aqueous solution.
Abstract: To improve the sensitivity of fluorescence detection to microwell plate to match the up-to-date bio-analysis, a simple and easy-to-access approach to efficiently sensitize the fluorescence detection to microwell plate was constructed. Taking the advantage of higher refractive index of soda lime glass than that of ambitious aqueous solution, several transparent soda lime glass microspheres were introduced into the wells on microwell plate to enhance the fluorescence detection before the generation of fluorophores. Around 2500 times enhancement of sensitivity for model resorufin was obtained through the microsphere enhanced fluorescence (MSEF), meanwhile, around 500 times lowered limitation of detection (LOD) was achieved in the detection of resorufin through the proposed MSEF. To proof the performance of MSEF in bio-measurement, the human IgA assay was implemented on the microwell plate coupled with MSEF. Around 70 times of lowered LOD could be obtained by utilizing the common microwell plate reader. To confirm the practicality of MSEF in the disease diagnosis, the measurements of human measles Ig G and human cancer marker carcinoembryonic antigen (CEA) were respectively performed by the microwell plate coupled MSEF. The sensitivities for human measles Ig G and for human cancer marker CEA were both greatly improved and those of LOD were lowered through the detections conducted by the fluorescence microscope or by the microwell plate reader. We expect the proposed MSEF could be a handy approach to improve the performance of microwell plate to widely benefit the operators of microwell plate.
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TL;DR: In this paper, an array-based high-throughput technique that facilitates gene expression and copy number surveys of very large numbers of tumors is presented. But, it is limited to a single tumor tissue microarray.
Abstract: Many genes and signalling pathways controlling cell proliferation, death and differentiation, as well as genomic integrity, are involved in cancer development. New techniques, such as serial analysis of gene expression and cDNA microarrays, have enabled measurement of the expression of thousands of genes in a single experiment, revealing many new, potentially important cancer genes. These genome screening tools can comprehensively survey one tumor at a time; however, analysis of hundreds of specimens from patients in different stages of disease is needed to establish the diagnostic, prognostic and therapeutic importance of each of the emerging cancer gene candidates. Here we have developed an array-based high-throughput technique that facilitates gene expression and copy number surveys of very large numbers of tumors. As many as 1000 cylindrical tissue biopsies from individual tumors can be distributed in a single tumor tissue microarray. Sections of the microarray provide targets for parallel in situ detection of DNA, RNA and protein targets in each specimen on the array, and consecutive sections allow the rapid analysis of hundreds of molecular markers in the same set of specimens. Our detection of six gene amplifications as well as p53 and estrogen receptor expression in breast cancer demonstrates the power of this technique for defining new subgroups of tumors.
4,164 citations
TL;DR: This work developed a method that, based on the Fourier Shift Theorem, computes all possible translations between pairs of 3D images, yielding the best overlap in terms of the cross-correlation measure and subsequently finds the globally optimal configuration of the whole group of3D images.
Abstract: Motivation: Modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-resolution 3D images, but is limited by a relatively small field of view compared with the size of large biological specimens. Therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (Stitching) of the whole image from individual image stacks.
Results: To optimally stitch a large collection of 3D confocal images, we developed a method that, based on the Fourier Shift Theorem, computes all possible translations between pairs of 3D images, yielding the best overlap in terms of the cross-correlation measure and subsequently finds the globally optimal configuration of the whole group of 3D images. This method avoids the propagation of errors by consecutive registration steps. Additionally, to compensate the brightness differences between tiles, we apply a smooth, non-linear intensity transition between the overlapping images. Our stitching approach is fast, works on 2D and 3D images, and for small image sets does not require prior knowledge about the tile configuration.
Availability: The implementation of this method is available as an ImageJ plugin distributed as a part of the Fiji project (FijiisjustImageJ: http://pacific.mpi-cbg.de/).
Contact: tomancak@mpi-cbg.de
1,989 citations
TL;DR: Fluorescence microscopy is making the transition to a quantitative and high-throughput technology to enable these techniques to be applied to functional genomics experiments.
Abstract: Fluorescence microscopy is a powerful tool to assay biological processes in intact living cells. Now, fluorescence microscopy is becoming a quantitative and high-throughput technology that can be applied to functional genomics experiments and can provide data for systems-biology approaches. In this post-genomic era, we need to define gene function on a genome-wide scale for model organisms and humans. The fundamental unit of biological processes is the cell. Among the most powerful tools to assay such processes in the physiological context of intact living cells are fluorescence microscopy and related imaging techniques. To enable these techniques to be applied to functional genomics experiments, fluorescence microscopy is making the transition to a quantitative and high-throughput technology.
422 citations
TL;DR: In this article, the authors report on their activities in design, fabrication, characterization and system integration of refractive microlens arrays for sensors and microsystems, including neural networks and multiple pupil imaging systems for photolithography.
Abstract: We report on our activities in design, fabrication, characterization and system integration of refractive microlens arrays for sensors and microsystems. Examples for chemical analysis systems (, blood gas sensor), neural networks and multiple pupil imaging systems for photolithography (microlens and smart mask lithography) are presented.
416 citations
TL;DR: This review describes how cellular imaging technologies contribute to the drug discovery process and addresses both high-content and high-throughput needs.
Abstract: Traditional screening paradigms often focus on single targets. To facilitate drug discovery in the more complex physiological environment of a cell or organism, powerful cellular imaging systems have been developed. The emergence of these detection technologies allows the quantitative analysis of cellular events and visualization of relevant cellular phenotypes. Cellular imaging facilitates the integration of complex biology into the screening process, and addresses both high-content and high-throughput needs. This review describes how cellular imaging technologies contribute to the drug discovery process.
335 citations