Carbon nanotube based high resolution holograms.

Carbon nanotubes are used as the smallest possible scattering element for diffracting light in a highly controlled manner to produce a 2D image. An array of carbon nanotubes is elegantly patterned to produce a high resolution hologram. In response to incident light on the hologram, a high contrast and wide field of view CAMBRIDGE image is produced.

Optical holograms based on carbon nanotubes

The size of pixels is one of the key limiting features in the state of the art of holographic displays systems. The resolution and field of view in these systems are dictated by the size of the pixel (the smallest light scattering element). We have demonstrated the utilization of carbon nanotubes (nanostructures) as the smallest possible scattering element for diffracting light in a highly controlled manner to produce a two dimensional image. An array of carbon nanotubes was elegantly patterned to produce a high resolution hologram. In response to the incident light on the hologram a high contrast image was produced. Due to the nanoscale dimension of the carbon nanotube array the image presented a wide field of view and high resolution. These results pave way towards the utilization of nanostructures for producing 3D holograms with wide field of view and high resolution. © 2013 IEEE.

Pixel-level tunable liquid crystal lenses for auto-stereoscopic display

Mobile video and gaming are now widely used, and delivery of a glass-free 3D experience is of both research and development interest. The key drawbacks of a conventional 3D display based on a static lenticular lenslet array and parallax barriers are low resolution, limited viewing angle and reduced brightness, mainly because of the need of multiple-pixels for each object point. This study describes the concept and performance of pixel-level cylindrical liquid crystal (LC) lenses, which are designed to steer light to the left and right eye sequentially to form stereo parallax. The width of the LC lenses can be as small as 20-30 μm, so that the associated auto-stereoscopic display will have the same resolution as the 2D display panel in use. Such a thin sheet of tunable LC lens array can be applied directly on existing mobile displays, and can deliver 3D viewing experience while maintaining 2D viewing capability. Transparent electrodes were laser patterned to achieve the single pixel lens resolution, and a high birefringent LC material was used to realise a large diffraction angle for a wide field of view. Simulation was carried out to model the intensity profile at the viewing plane and optimise the lens array based on the measured LC phase profile. The measured viewing angle and intensity profile were compared with the simulation results. © 2014 SPIE.

A static polarization imaging spectrometer based on a Savart polariscope

This paper describes the design of an interference imaging spectrometer. A static Polarization Imaging Spectrometer (PIS) based on a single Savart polariscope has been developed. It produces the interferogram and target's image in the spatial domain which are recorded by using a two-dimensional (2D) CCD detector. Imaging lens localizes the interference fringes and target's image coincident with the plane of detector, thereby facilitating an extremely compact design. The spectrum of the input light is reconstructed through the Fourier-transform of the interferogram. The total optics is as small as 20 x 6 cm phi in size and the spectral resolution of the prototype system is 97.66 cm(-1) between 25,000 and 10, 000 cm(-1). The polarization interference imaging device has advantages of ultra-compact size, wide field of view, high throughput and without any moving parts. (C) 2002 Published by Elsevier Science B.V.

Total-internal-reflection fluorescence microscopy with W-shaped axicon mirrors

A scheme based on a W-shaped axicon mirror device for total-internal-reflection fluorescence microscopy (TIRFM) is presented. This approach combines the advantages of higher efficiency compared with traditional TIRFM, adjustable illumination area, and simple switching between wide-field and TIRF imaging modes. TIRF images obtained with this approach are free of shadow artifacts and of interference fringes. Example micrographs of fluorescently labeled polystyrene beads, of Convallaria majalis tissue, and of Propidium-iodide-labeled Chinese hamster ovary cells are shown, and the capabilities of the scheme are discussed. (C) 2010 Optical Society of America

accurate and self-consistent ocean color algorithm:simultaneous retrieval of aerosol optical properties and chlorphyll concentrations

A new algorithm has been developed for simultaneous retrieval of aerosol optical properties and chlorophyll concentrations in case I waters. This algorithm is based on an improved complete model for the inherent optical properties and accurate simulations of the radiative transfer process in the coupled atmosphere-ocean system. It has been tested against synthetic radiances generated for the Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) channels and has been shown to be robust and accurate. A unique feature of this algorithm is that it uses the measured radiances in both near-IR and visible channels to find that combination of chlorophyll concentration and aerosol optical properties that minimizes the error across the spectrum. Thus the error in the retrieved quantities can be quantified.

Multiscale optics for enhanced light collection from a point source.

High-efficiency collection of photons emitted by a point source over a wide field of view (FoV) is crucial for many applications. Multiscale optics offer improved light collection by utilizing small optical components placed close to the optical source, while maintaining a wide FoV provided by conventional imaging optics. In this work, we demonstrate collection efficiency of 26% of photons emitted by a pointlike source using a micromirror fabricated in silicon with no significant decrease in collection efficiency over a 10 mm object space.

Intraoperative spectral domain optical coherence tomography for vitreoretinal surgery.

We demonstrate in vivo human retinal imaging using an intraoperative microscope-mounted optical coherence tomography system (MMOCT). Our optomechanical design adapts an Oculus Binocular Indirect Ophthalmo Microscope (BIOM3), suspended from a Leica ophthalmic surgical microscope, with spectral domain optical coherence tomography (SD-OCT) scanning and relay optics. The MMOCT enables wide-field noncontact real-time cross-sectional imaging of retinal structure, allowing for SD-OCT augmented intrasurgical microscopy for intraocular visualization. We experimentally quantify the axial and lateral resolution of the MMOCT and demonstrate fundus imaging at a 20Hz frame rate.

Enhancing imaging systems using transformation optics.

We apply the transformation optical technique to modify or improve conventional refractive and gradient index optical imaging devices. In particular, when it is known that a detector will terminate the paths of rays over some surface, more freedom is available in the transformation approach, since the wave behavior over a large portion of the domain becomes unimportant. For the analyzed configurations, quasi-conformal and conformal coordinate transformations can be used, leading to simplified constitutive parameter distributions that, in some cases, can be realized with isotropic index; index-only media can be low-loss and have broad bandwidth. We apply a coordinate transformation to flatten a Maxwell fish-eye lens, forming a near-perfect relay lens; and also flatten the focal surface associated with a conventional refractive lens, such that the system exhibits an ultra-wide field-of-view with reduced aberration.

Micro-Anatomical Quantitative Imaging Towards Enabling Automated Diagnosis of Thick Tissues at the Point of Care

Histopathology is the clinical standard for tissue diagnosis. However, histopathology has several limitations including that it requires tissue processing, which can take 30 minutes or more, and requires a highly trained pathologist to diagnose the tissue. Additionally, the diagnosis is qualitative, and the lack of quantitation leads to possible observer-specific diagnosis. Taken together, it is difficult to diagnose tissue at the point of care using histopathology.

Several clinical situations could benefit from more rapid and automated histological processing, which could reduce the time and the number of steps required between obtaining a fresh tissue specimen and rendering a diagnosis. For example, there is need for rapid detection of residual cancer on the surface of tumor resection specimens during excisional surgeries, which is known as intraoperative tumor margin assessment. Additionally, rapid assessment of biopsy specimens at the point-of-care could enable clinicians to confirm that a suspicious lesion is successfully sampled, thus preventing an unnecessary repeat biopsy procedure. Rapid and low cost histological processing could also be potentially useful in settings lacking the human resources and equipment necessary to perform standard histologic assessment. Lastly, automated interpretation of tissue samples could potentially reduce inter-observer error, particularly in the diagnosis of borderline lesions.

To address these needs, high quality microscopic images of the tissue must be obtained in rapid timeframes, in order for a pathologic assessment to be useful for guiding the intervention. Optical microscopy is a powerful technique to obtain high-resolution images of tissue morphology in real-time at the point of care, without the need for tissue processing. In particular, a number of groups have combined fluorescence microscopy with vital fluorescent stains to visualize micro-anatomical features of thick (i.e. unsectioned or unprocessed) tissue. However, robust methods for segmentation and quantitative analysis of heterogeneous images are essential to enable automated diagnosis. Thus, the goal of this work was to obtain high resolution imaging of tissue morphology through employing fluorescence microscopy and vital fluorescent stains and to develop a quantitative strategy to segment and quantify tissue features in heterogeneous images, such as nuclei and the surrounding stroma, which will enable automated diagnosis of thick tissues.

To achieve these goals, three specific aims were proposed. The first aim was to develop an image processing method that can differentiate nuclei from background tissue heterogeneity and enable automated diagnosis of thick tissue at the point of care. A computational technique called sparse component analysis (SCA) was adapted to isolate features of interest, such as nuclei, from the background. SCA has been used previously in the image processing community for image compression, enhancement, and restoration, but has never been applied to separate distinct tissue types in a heterogeneous image. In combination with a high resolution fluorescence microendoscope (HRME) and a contrast agent acriflavine, the utility of this technique was demonstrated through imaging preclinical sarcoma tumor margins. Acriflavine localizes to the nuclei of cells where it reversibly associates with RNA and DNA. Additionally, acriflavine shows some affinity for collagen and muscle. SCA was adapted to isolate acriflavine positive features or APFs (which correspond to RNA and DNA) from background tissue heterogeneity. The circle transform (CT) was applied to the SCA output to quantify the size and density of overlapping APFs. The sensitivity of the SCA+CT approach to variations in APF size, density and background heterogeneity was demonstrated through simulations. Specifically, SCA+CT achieved the lowest errors for higher contrast ratios and larger APF sizes. When applied to tissue images of excised sarcoma margins, SCA+CT correctly isolated APFs and showed consistently increased density in tumor and tumor + muscle images compared to images containing muscle. Next, variables were quantified from images of resected primary sarcomas and used to optimize a multivariate model. The sensitivity and specificity for differentiating positive from negative ex vivo resected tumor margins was 82% and 75%. The utility of this approach was further tested by imaging the in vivo tumor cavities from 34 mice after resection of a sarcoma with local recurrence as a bench mark. When applied prospectively to images from the tumor cavity, the sensitivity and specificity for differentiating local recurrence was 78% and 82%. The results indicate that SCA+CT can accurately delineate APFs in heterogeneous tissue, which is essential to enable automated and rapid surveillance of tissue pathology.

Two primary challenges were identified in the work in aim 1. First, while SCA can be used to isolate features, such as APFs, from heterogeneous images, its performance is limited by the contrast between APFs and the background. Second, while it is feasible to create mosaics by scanning a sarcoma tumor bed in a mouse, which is on the order of 3-7 mm in any one dimension, it is not feasible to evaluate an entire human surgical margin. Thus, improvements to the microscopic imaging system were made to (1) improve image contrast through rejecting out-of-focus background fluorescence and to (2) increase the field of view (FOV) while maintaining the sub-cellular resolution needed for delineation of nuclei. To address these challenges, a technique called structured illumination microscopy (SIM) was employed in which the entire FOV is illuminated with a defined spatial pattern rather than scanning a focal spot, such as in confocal microscopy.

Thus, the second aim was to improve image contrast and increase the FOV through employing wide-field, non-contact structured illumination microscopy and optimize the segmentation algorithm for new imaging modality. Both image contrast and FOV were increased through the development of a wide-field fluorescence SIM system. Clear improvement in image contrast was seen in structured illumination images compared to uniform illumination images. Additionally, the FOV is over 13X larger than the fluorescence microendoscope used in aim 1. Initial segmentation results of SIM images revealed that SCA is unable to segment large numbers of APFs in the tumor images. Because the FOV of the SIM system is over 13X larger than the FOV of the fluorescence microendoscope, dense collections of APFs commonly seen in tumor images could no longer be sparsely represented, and the fundamental sparsity assumption associated with SCA was no longer met. Thus, an algorithm called maximally stable extremal regions (MSER) was investigated as an alternative approach for APF segmentation in SIM images. MSER was able to accurately segment large numbers of APFs in SIM images of tumor tissue. In addition to optimizing MSER for SIM image segmentation, an optimal frequency of the illumination pattern used in SIM was carefully selected because the image signal to noise ratio (SNR) is dependent on the grid frequency. A grid frequency of 31.7 mm-1 led to the highest SNR and lowest percent error associated with MSER segmentation.

Once MSER was optimized for SIM image segmentation and the optimal grid frequency was selected, a quantitative model was developed to diagnose mouse sarcoma tumor margins that were imaged ex vivo with SIM. Tumor margins were stained with acridine orange (AO) in aim 2 because AO was found to stain the sarcoma tissue more brightly than acriflavine. Both acriflavine and AO are intravital dyes, which have been shown to stain nuclei, skeletal muscle, and collagenous stroma. A tissue-type classification model was developed to differentiate localized regions (75x75 µm) of tumor from skeletal muscle and adipose tissue based on the MSER segmentation output. Specifically, a logistic regression model was used to classify each localized region. The logistic regression model yielded an output in terms of probability (0-100%) that tumor was located within each 75x75 µm region. The model performance was tested using a receiver operator characteristic (ROC) curve analysis that revealed 77% sensitivity and 81% specificity. For margin classification, the whole margin image was divided into localized regions and this tissue-type classification model was applied. In a subset of 6 margins (3 negative, 3 positive), it was shown that with a tumor probability threshold of 50%, 8% of all regions from negative margins exceeded this threshold, while over 17% of all regions exceeded the threshold in the positive margins. Thus, 8% of regions in negative margins were considered false positives. These false positive regions are likely due to the high density of APFs present in normal tissues, which clearly demonstrates a challenge in implementing this automatic algorithm based on AO staining alone.

Thus, the third aim was to improve the specificity of the diagnostic model through leveraging other sources of contrast. Modifications were made to the SIM system to enable fluorescence imaging at a variety of wavelengths. Specifically, the SIM system was modified to enabling imaging of red fluorescent protein (RFP) expressing sarcomas, which were used to delineate the location of tumor cells within each image. Initial analysis of AO stained panels confirmed that there was room for improvement in tumor detection, particularly in regards to false positive regions that were negative for RFP. One approach for improving the specificity of the diagnostic model was to investigate using a fluorophore that was more specific to staining tumor. Specifically, tetracycline was selected because it appeared to specifically stain freshly excised tumor tissue in a matter of minutes, and was non-toxic and stable in solution. Results indicated that tetracycline staining has promise for increasing the specificity of tumor detection in SIM images of a preclinical sarcoma model and further investigation is warranted.

In conclusion, this work presents the development of a combination of tools that is capable of automated segmentation and quantification of micro-anatomical images of thick tissue. When compared to the fluorescence microendoscope, wide-field multispectral fluorescence SIM imaging provided improved image contrast, a larger FOV with comparable resolution, and the ability to image a variety of fluorophores. MSER was an appropriate and rapid approach to segment dense collections of APFs from wide-field SIM images. Variables that reflect the morphology of the tissue, such as the density, size, and shape of nuclei and nucleoli, can be used to automatically diagnose SIM images. The clinical utility of SIM imaging and MSER segmentation to detect microscopic residual disease has been demonstrated by imaging excised preclinical sarcoma margins. Ultimately, this work demonstrates that fluorescence imaging of tissue micro-anatomy combined with a specialized algorithm for delineation and quantification of features is a means for rapid, non-destructive and automated detection of microscopic disease, which could improve cancer management in a variety of clinical scenarios.

Variations of chlorophyll-a in the northeastern Indian Ocean after the 2004 South Asian tsunami

Analysis of satellite remote sensing data has revealed changes in distribution of chlorophyll-a (Chl-a) and sea surface temperature (SST) in the Indian Ocean during the South Asian tsunami in December 2004. Chl-a data derived from Moderate Resolution Imaging Spectroradiometer (MODIS) and Sea-viewing Wide Field-ofview Sensor (SeaWiFS) images were examined for the period from 1998 to 2005. Around the epicentre of the Sumatra earthquake, the Chl-a concentrationwas found to increase prior to the main event on 26 December 2004 and then decrease during the tsunami event, while a high SST (~30-31°C) was observed in and around the epicentral region. Chl-a concentrations in the coastal waters of the Southeast Asian countries were remarkably low during and after the tsunami. Similar but relatively small variations inChl-a and SST were observed during the second earthquake on 28 March 2005. Analysis of Chl-a, SST, wind and upwelling water has provided information for understanding the changes in Chl-a concentration during the tsunami. A very large offshore phytoplankton bloom (~300 km2) appeared to the southeast of Sri Lanka about 3 weeks after the tsunami; this might have been caused by a tropical storm that could be responsible for the enhancement of nutrients. © 2009 Taylor & Francis.

Space-borne study of seasonal, multi-year, and decadal phytoplankton dynamics in the Bay of Biscay

Seasonal and inter-annual variations in phytoplankton community abundance in the Bay of Biscay are studied. Preliminarily processed by the National Aeronautics and Space Administration (NASA) to yield normalized water-leaving radiance and the top-of-the-atmosphere solar radiance, Sea-viewing Wide Field-of-View Sensor (SeaWiFS), Moderate Resolution Imaging Spectroradiometer (MODIS), and Coastal Zone Color Scanner (CZCS) data are further supplied to our dedicated retrieval algorithms to infer the sought for parameters. By applying the National Oceanic and Atmospheric Administration's (NOAA's) Advanced Very High Resolution Radiometer (AVHRR) data, the surface reflection coefficient in the only band in the visible spectrum is derived and employed for analysis. Decadal bridged time series of variations of diatom-dominated phytoplankton and green dinoflagellate Lepidodinium chlorophorum within the shelf zone and the coccolithophore Emiliania huxleyi in the pelagic area of the Bay are documented and analysed in terms of impacts of some biogeochemical and geophysical forcing factors.

Coccolithophore surface distributions in the North Atlantic and their modulation of the air-sea flux of CO2 from 10 years of satellite Earth observation data

Coccolithophores are the primary oceanic phytoplankton responsible for the production of calcium carbonate (CaCO3). These climatically important plankton play a key role in the oceanic carbon cycle as a major contributor of carbon to the open ocean carbonate pump (similar to 50 %) and their calcification can affect the atmosphere-to-ocean (air-sea) uptake of carbon dioxide (CO2) through increasing the seawater partial pressure of CO2 (pCO(2)). Here we document variations in the areal extent of surface blooms of the globally important coccolithophore, Emiliania huxleyi, in the North Atlantic over a 10-year period (1998-2007), using Earth observation data from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS). We calculate the annual mean sea surface areal coverage of E. huxleyi in the North Atlantic to be 474 000 +/- 104 000 km(2), which results in a net CaCO3 carbon (CaCO3-C) production of 0.14-1.71 Tg CaCO3-C per year. However, this surface coverage (and, thus, net production) can fluctuate inter-annually by -54/+81% about the mean value and is strongly correlated with the El Nino/Southern Oscillation (ENSO) climate oscillation index (r = 0.75, p < 0.02). Our analysis evaluates the spatial extent over which the E. huxleyi blooms in the North Atlantic can increase the pCO(2) and, thus, decrease the localised air-sea flux of atmospheric CO2. In regions where the blooms are prevalent, the average reduction in the monthly air-sea CO2 flux can reach 55%. The maximum reduction of the monthly air-sea CO2 flux in the time series is 155 %. This work suggests that the high variability, frequency and distribution of these calcifying plankton and their impact on pCO(2) should be considered if we are to fully understand the variability of the North Atlantic air-to-sea flux of CO2. We estimate that these blooms can reduce the annual N. Atlantic net sink atmospheric CO2 by between 3-28 %.

From silk to satellite: half a century of ocean colour anomalies in the Northeast Atlantic

Changes in phytoplankton dynamics influence marine biogeochemical cycles, climate processes, and food webs, with substantial social and economic consequences. Large-scale estimation of phytoplankton biomass was possible via ocean colour measurements from two remote sensing satellites – the Coastal Zone Color Scanner (CZCS, 1979-1986) and the Sea-viewing Wide Field-of-view Sensor (SeaWiFS, 1998-2010). Due to the large gap between the two satellite eras and differences in sensor characteristics, comparison of the absolute values retrieved from the two instruments remains challenging. Using a unique in situ ocean colour dataset that spans more than half a century, the two satellite-derived chlorophyll-a (Chl-a) eras are linked to assess concurrent changes in phytoplankton variability and bloom timing over the Northeast Atlantic Ocean and North Sea. Results from this unique re-analysis reflect a clear increasing pattern of Chl-a, a merging of the two seasonal phytoplankton blooms producing a longer growing season and higher seasonal biomass, since the mid-1980s. The broader climate plays a key role in Chl-a variability as the ocean colour anomalies parallel the oscillations of the Northern Hemisphere Temperature (NHT) since 1948.

Composite front maps for improved visibility of dynamic sea-surface features on cloudy SeaWiFS and AVHRR data

Novel techniques have been developed for increasing the value of cloud-affected sequences of Advanced Very High Resolution Radiometer (AVHRR) sea-surface temperature (SST) data and Sea-viewing Wide Field-of-view Sensor (SeaWiFS) ocean colour data for visualising dynamic physical and biological oceanic processes such as fronts, eddies and blooms. The proposed composite front map approach is to combine the location, strength and persistence of all fronts observed over several days into a single map, which allows intuitive interpretation of mesoscale structures. This method achieves a synoptic view without blurring dynamic features, an inherent problem with conventional time-averaging compositing methods. Objective validation confirms a significant improvement in feature visibility on composite maps compared to individual front maps. A further novel aspect is the automated detection of ocean colour fronts, correctly locating 96% of chlorophyll fronts in a test data set. A sizeable data set of 13,000 AVHRR and 1200 SeaWiFS scenes automatically processed using this technique is applied to the study of dynamic processes off the Iberian Peninsula such as mesoscale eddy generation, and many additional applications are identified. Front map animations provide a unique insight into the evolution of upwelling and eddies.