Synthetic data framework to estimate the minimum detectable concentration of contrast agents for multispectral optoacoustic imaging of small animals

The concentrations of contrast agents for optoacoustic imaging of small animals must usually be optimized through extensive pilot experiments on a case‐by‐case basis. The present work describes a streamlined approach for determining the minimum detectable concentration (MDC) of a contrast agent given experimental conditions and imaging system parameters. The developed Synthetic Data Framework (SDF) allows estimation of MDCs of various contrast agents under different tissue conditions without extensive animal experiments. The SDF combines simulated optoacoustic signals from exogenously administered contrast agents with in vivo experimental signals from background tissue to generate realistic synthetic multispectral optoacoustic images. In this paper, the SDF is validated with in vivo measurements and demonstrates close agreement between SDF synthetic data and experimental data in terms of both image intensity and MDCs. Use of the SDF to estimate MDCs for fluorescent dyes and nanoparticles at different tissue depths and for imaging lesions of different sizes is illustrated.     

Environment‐specific spectral modeling: A new tool for the analysis of biological specimens

The recent discovery of fluorescent dyes for improving pathologic tissues identification has highlighted the need of robust methods for performance validation especially in the field of fluorescence‐guided surgery. Optical imaging of excised tissue samples is the reference tool to validate the association between dyes localization and the underlying histology in a controlled environment. Spectral unmixing may improve the validation process discriminating dye from endogenous signal. Here, an innovative spectral modeling approach that weights the spectral shifts associated with changes in chemical environment is described. The method is robust against spectral shift variations and its application leads to unbiased spectral weights estimates as demonstrated by numerical simulations. Finally, spectral shifts values computed pixel‐wise from spectral images are used to display additional information with potential diagnostic value.      

基于遥感数据源的景观分析系统的设计与实现

在Ｖｉｓｕａｌ Ｃ＋＋环境下,设计并实现了一个景观分析系统。该系统采用提取斑块边界象素集的方法,提高了斑块搜索的速度,而且提供了斑块间距离计算、相邻斑块间边界长度计算等景观分析功能。该系统被应用到北京西北郊同分析中。通过分析表明,该系统不仅能计算面积、周长、中心坐标和最近同类型斑块的距离等单个斑块指数,而且能在此基础上计算景观类型和整个景观层次上的各种指数,从而弥补了目前多数地理信息系统在分析应用     

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Current methods in DNA nano-architecture have successfully engineered a variety of 2D and 3D structures using principles of self-assembly. In this article, we describe detailed protocols on how to fabricate sophisticated 2D shapes through the self-assembly of uniquely addressable single-stranded DNA tiles which act as molecular pixels on a molecular canvas. Each single-stranded tile (SST) is a 42-nucleotide DNA strand composed of four concatenated modular domains which bind to four neighbors during self-assembly. The molecular canvas is a rectangle structure self-assembled from SSTs. A prescribed complex 2D shape is formed by selecting the constituent molecular pixels (SSTs) from a 310-pixel molecular canvas and then subjecting the corresponding strands to one-pot annealing. Due to the modular nature of the SST approach we demonstrate the scalability, versatility and robustness of this method. Compared with alternative methods, the SST method enables a wider selection of information polymers and sequences through the use of de novo designed and synthesized short DNA strands.     

Front Cover: A theoretical‐experimental methodology for assessing the sensitivity of biomedical spectral imaging platforms,assays, and analysis methods (J. Biophotonics 1/2018)

A hyperspectral image data cube acquired from HEK‐293 cells labeled with cytoplasmic and nuclear stains: Calcein Green and NucBlu. The top view (XY plane) displays three spectrally unmixed channels for cellular autofluorescence (red), Calcein Green (green), and NucBlue (blue). The Z axis shows spectral information, from low to high wavelength. The article by Leavesley and colleagues describes an approach for calculating the sensitivity of spectral imaging assays for detecting a fluorescence signature within a mix of other signatures or autofluorescence. Further details can be found in the article by Silas J. Leavesley et al. ( e201600227 ).

     

近17年陕西榆林植被指数的时空变化及影响因素

植被指数是研究区域植被变化的重要手段。基于MODIS/Terra NDVI遥感影像数据,对陕西榆林市2000—2016年8月份NDVI进行像元尺度的时空变化及影响因素分析。结果表明,榆林有96.44%的区域植被指数是增加的,增加值在0—0.02/a区域面积占榆林的93.63%,呈显著增加趋势的面积占榆林的80.72%。复直线回归分析显示,气象因素对植被生长、演化起到了促进作用,人类活动使得植被指数等级变得更加均匀。人类活动抑制植被生长演化的区域占榆林总面积的45.04%,主要分布在榆林市最北部的府谷县、榆林市南部及西部的大部分区域;人类活动促使植被指数增加的区域占榆林总面积的54.96%,说明有一半以上的区域,人类活动对植被生长起到了促进作用,这些地区的封山育林、退耕还林、退牧还草等措施的实施效果较好。     

基于MODIS-EVI的重庆植被覆盖时空分异特征研究

利用MODIS-EVI数据,采用像元二分模型结合距平百分率、变异系数和分布指数对2000—2015年重庆植被覆盖度变化时空分异特征进行了分析,结果表明:(1)重庆植被年际、夏、秋季和2008—2015年春季以中覆盖度为主,冬季以及2000—2007年春季以低覆盖度为主。(2)植被覆盖年际变化不明显;劣覆盖度在2000、2002、2003年春季,2001、2006年秋季以及2011年冬季异常偏多;低覆盖度在2000、2001年秋季异常偏多;高覆盖度在2000、2008年秋季和2014年春季异常偏少。(3)植被的波动变化除了冬季以中度为主外,年际、春、夏、秋季均以轻度为主;稳定比例最高为夏季,轻度比例最高为秋季,中度和重度比例最高为冬季。(4)稳定和轻度波动类型主要分布在山地森林和草地区,中度和重度波动类型主要是城镇、水域及其周边区域。在400m以下,植被变化为重度波动;在400—800m,植被年际和夏季趋于稳定分布,而春、秋、冬季为轻度波动;在800—1300m,植被年际和夏季为中度波动,春、秋、冬季为稳定分布;在1300m以上,植被年际和夏季呈现轻度波动,春季为中度波动,秋、冬季为稳定分布。     

黄土高原近10年植被覆盖的动态变化及驱动力

基于Timesat的非对称高斯函数(AG)拟合法重建MODIS-NDVI数据,利用像元二分模型估算了黄土高原近10年的植被覆盖度(VC),并分析了年植被覆盖度的变化趋势和其与降水温度的相关性。研究结果表明:黄土高原植被覆盖度总体上呈现东南高西北低、由东南向西北递减的特征。其中森林生态系统平均覆盖度最高,灌木、草地生态系统次之,荒漠生态系统最低,空间差异明显。2010年森林生态系统植被覆盖度达到81.6%,主要包括太行山、吕梁山和秦岭地区。暖温带森林区植被组成以落叶阔叶林为主,覆盖度常年较高,为80%以上。西北部温带草原区,植被覆盖度达到38.8%。温带草地主要依水分梯度,由东南到西北分布有以旱生性多年生草本植物为主的典型草原,植被覆盖度呈现相应的递减趋势。黄土高原总面积78.6%的地区年植被覆盖度呈增加趋势;而占总面积19.4%的地区年植被覆盖度呈下降趋势。在空间分布上,植被覆盖度显著增加的区域主要分布在榆林至延安周边地区和秦岭一带;植被覆盖度显著减少区域沿兰州至银川呈条带状分布。     

Rapid plant diversity assessment using a pixel nested plot design: A case study in Beaver Meadows, Rocky Mountain National Park, Colorado, USA

Geospatial statistical modelling and thematic maps have recently emerged as effective tools for the management of natural areas at the landscape scale. Traditional methods for the collection of field data pertaining to questions of landscape were developed without consideration for the parameters of these applications. We introduce an alternative field sampling design based on smaller unbiased random plot and subplot locations called the pixel nested plot (PNP). We demonstrate the applicability of the PNP design of 15 m × 15 m to assess patterns of plant diversity and species richness across the landscape at Rocky Mountain National Park (RMNP), Colorado, USA in a time (cost)-efficient manner for field data collection. Our results produced comparable results to a previous study in the Beaver Meadow study (BMS) area within RMNP, where there was a demonstrated focus of plant diversity. Our study used the smaller PNP sampling design for field data collection which could be linked to geospatial information data and could be used for landscape-scale analyses and assessment applications. In 2003, we established 61 PNP in the eastern region of RMNP. We present a comparison between this approach using a sub-sample of 19 PNP from this data set and 20 of Modified Whittaker nested plots (MWNP) of 20 m × 50 m that were collected in the BMS area. The PNP captured 266 unique plant species while the MWNP captured 275 unique species. Based on a comparison of PNP and MWNP in the Beaver Meadows area, RMNP, the PNP required less time and area sampled to achieve a similar number of species sampled. Using the PNP approach for data collection can facilitate the ecological monitoring of these vulnerable areas at the landscape scale in a time- and therefore cost-effective manner.     

1994-2016年和田绿洲植被覆盖时空变化分析

监测植被变化对评价区域生态环境质量及生态过程具有重要意义。基于Landsat数据影像,运用归一化植被指数、像元二分模型、重心迁移模型等方法分析和田绿洲植被覆盖时空变化。结果表明：（1）和田绿洲植被分布总体以玉龙喀什河和喀拉喀什河为轴线,从高到低向外展布,高覆被以大面积片状集中于绿洲中部,低、中覆被相对零散围绕高覆被分布;（2）过去23年,和田绿洲植被覆盖面积和植被覆盖度均呈升高趋势。2016年相比1994年,绿洲植被覆盖面积增加553 km²,增长了19.6%;（3）和田绿洲覆被变化存在阶段性和区域性差异。时段上,2000-2005年覆被面积增加最明显;区域上,西部覆被增加最显著;（4）气候变化对和田绿洲覆被变化存在一定影响,但人类活动影响最直接。其中耕地开垦、作物种植是和田绿洲覆被增加的最主要因素,而城市基建是引起绿洲覆被减少的最主要因素。同时,因农耕区水耗增加挤占天然覆被生态用水,引起天然覆被退化,威胁绿洲未来发展;（5）过去23年,绿洲覆被重心整体西移。