An adaptive microscope for the imaging of biological surfaces

Scanning fluorescence microscopes are now able to image large biological samples at high spatial and temporal resolution. This comes at the expense of an increased light dose which is detrimental to fluorophore stability and cell physiology. To highly reduce the light dose, we designed an adaptive scanning fluorescence microscope with a scanning scheme optimized for the unsupervised imaging of cell sheets, which underly the shape of many embryos and organs. The surface of the tissue is first delineated from the acquisition of a very small subset (~0.1%) of sample space, using a robust estimation strategy. Two alternative scanning strategies are then proposed to image the tissue with an improved photon budget, without loss in resolution. The first strategy consists in scanning only a thin shell around the estimated surface of interest, allowing high reduction of light dose when the tissue is curved. The second strategy applies when structures of interest lie at the cell periphery (e.g. adherens junctions). An iterative approach is then used to propagate scanning along cell contours. We demonstrate the benefit of our approach imaging live epithelia from Drosophila melanogaster. On the examples shown, both approaches yield more than a 20-fold reduction in light dose -and up to more than 80-fold- compared to a full scan of the volume. These smart-scanning strategies can be easily implemented on most scanning fluorescent imaging modality. The dramatic reduction in light exposure of the sample should allow prolonged imaging of the live processes under investigation.

Focused X-ray Luminescence Computed Tomography using a Continuous Scanning Scheme

X-ray luminescence computed tomography (XLCT) imaging is a hybrid molecular imaging modality combining the merits of both conventional x-ray imaging (high spatial resolution) and optical imaging (high measurement sensitivity). The narrow x-ray beam based XLCT imaging has been shown to be promising. However due to the selective excitation scheme, the imaging speed is slow thus limiting its practical applications for in vivo imaging. In this work, we have introduced a continuous scanning scheme to acquire data for each angular projection in one motion, eliminating the previous stepping scheme and reducing the data acquisition time, which makes it feasible for multiple transverse scans for three-dimensional (3D) imaging. We have introduced a high accuracy vertical stage to our focused x-ray beam based XLCT imaging system to perform high-resolution and 3D XLCT imaging. We have also included a scintillator crystal coupled to a PMT to act as a single-pixel detector for boundary detection purposes to replace our previous flat panel x-ray detector. We have verified the feasibility of our proposed scanning scheme and imaging system by performing phantom experimental studies. A phantom was embedded with a set of cylindrical targets with 200 µm edge-to-edge distance and was scanned in our imaging system with the proposed method. To test the feasibility for 3D scanning, we took measurements from 4 transverse slices with a vertical step size of 1 mm. The results of the experiments verified the feasibility of our proposed method to perform 3D XLCT imaging using a narrow x-ray beam in a reasonable time.

High-Contrast and -Resolution 3-D Ultrasonography with a Clinical Linear Transducer Array Scanned in a Rotate-Translate Geometry

We proposed a novel solution for volumetric ultrasound imaging using single-side access 3-D synthetic aperture scanning of a clinical linear array. This solution is based on an advanced scanning geometry and a software-based ultrasound platform. The rotate-translate scanning scheme increases the elevation angular aperture by pivoting the array (−45° to 45°) around its array axis (axis along the row of its elements) and then scans the imaged object for each pivoted angle by translating the array perpendicularly to the rotation axis. A theoretical basis is presented so that the angular and translational scan sampling periods can be best adjusted for any linear transducer array. We experimentally implemented scanning with a 5-MHz array. In vitro characterization was performed with phantoms designed to test resolution and contrast. Spatial resolution assessed based on the full-width half-maximum of images from isolated microspheres was increased by a factor of 3 along the translational direction from a simple translation scan of the array. Moreover, the resolution was uniform over a cross-sectional area of 4.5 cm2. Angular sampling periods were optimized and tapered to decrease the scan duration while maintaining image contrast (contrast at the center of a 5-mm cyst on the order of −26 dB for 4° angular period and a scan duration of 10 s for a 9-cm3 volume). We demonstrated that superior 3-D ultrasound imaging can be obtained with a clinical array using our scanning strategy. This technique offers a promising and flexible alternative to development of costly matrix arrays toward the development of sensitive volumetric ultrasonography.

Optimization of Scanning Scheme for Low-height Vegetation Survey Based on Terrestrial Laser Scanning - A Case Study on the Restored Sand Land, Southern Qinghai-Tibetan Plateau

Background: In recent decades, vegetation surveys based on terrestrial laser scanning (TLS) have developed rapidly, especially on the forest inventory, but few studies have been conducted to the low-height vegetation. Because of the high investigation cost and subjectivity, it is impending to provide a scientific scanning scheme based on the TLS for the low-height vegetation survey (e.g. shrub, grassland, and meadow) in eco-fragile region (e.g. Qinghai-Tibetan Plateau). Method: In this study, we extracted the vegetation parameter i.e., number, height (H), and crown width (CW) of the two sample plots to evaluate the integrity of the data collected by TLS, on the restored sand land in southern Qinghai-Tibetan Plateau. We assessed the difference between the scanning mode of single-scan (SS) and multiple-scan (MS), and evaluated the influence of terrain fluctuation (windward slope, leeward slope, and the peak of slope) on the determination of scanning spots.Results: The results showed that: (1) the accuracy of vegetation parameter extracted by the mode of SS was mainly affected by the occlusion and the distance from central scanning spot, the RMSE of vegetation parameters is the smallest (RMSEH = 0.186 m; RMSECW = 0.208 m) within 20 m from the central scanning spot. (2) For the MS mode, in addition to the central scanning spot, the scanning spot located at the peak of the slope is the most important, which was the connection of combining the data of windward slope and leeward slope.Conclusion: To sum up, the scientific layout of scanning spot is the key to collecting data by TLS efficiently, and topography is the main factor affecting the layout of scanning spot. Since occlusion effect cannot be avoided, it can only be compensated by setting up more scanning points. Secondly, the accuracy of different sensors will has influence on the distance between adjacent scanning spots.