Analysis‐preserving video microscopy compression via correlation and mathematical morphology

The large amount video data produced by multi‐channel, high‐resolution microscopy system drives the need for a new high‐performance domain‐specific video compression technique. We describe a novel compression method for video microscopy data. The method is based on Pearson's correlation and mathematical morphology. The method makes use of the point‐spread function (PSF) in the microscopy video acquisition phase. We compare our method to other lossless compression methods and to lossy JPEG, JPEG2000, and H.264 compression for various kinds of video microscopy data including fluorescence video and brightfield video. We find that for certain data sets, the new method compresses much better than lossless compression with no impact on analysis results. It achieved a best compressed size of 0.77% of the original size, 25× smaller than the best lossless technique (which yields 20% for the same video). The compressed size scales with the video's scientific data content. Further testing showed that existing lossy algorithms greatly impacted data analysis at similar compression sizes. Microsc. Res. Tech. 78:1055–1061, 2015. © 2015 Wiley Periodicals, Inc.     

Image compression and data integrity in confocal microscopy

To manage large volumes of image data generated routinely using real-time confocal microscopy, compressing image data using a lossy algorithm prior to sustained video rate transferring and/or storing is proposed. Test criteria for determining the acceptability of uncompressed data, both qualitatively and quantitatively, are described, and an empirical demonstration of the use of lossy compression in data management is provided. It is found that, if appropriately used, the lossy compression scheme could retain all the useful information in the data while providing better compression ratios (memory for the original/ memory for the compressed) when compared with a lossless scheme.     

Out‐of‐focus background subtraction for fast structured illumination super‐resolution microscopy of optically thick samples

We propose a structured illumination microscopy method to combine super resolution and optical sectioning in three‐dimensional (3D) samples that allows the use of two‐dimensional (2D) data processing. Indeed, obtaining super‐resolution images of thick samples is a difficult task if low spatial frequencies are present in the in‐focus section of the sample, as these frequencies have to be distinguished from the out‐of‐focus background. A rigorous treatment would require a 3D reconstruction of the whole sample using a 3D point spread function and a 3D stack of structured illumination data. The number of raw images required, 15 per optical section in this case, limits the rate at which high‐resolution images can be obtained. We show that by a succession of two different treatments of structured illumination data we can estimate the contrast of the illumination pattern and remove the out‐of‐focus content from the raw images. After this cleaning step, we can obtain super‐resolution images of optical sections in thick samples using a two‐beam harmonic illumination pattern and a limited number of raw images. This two‐step processing makes it possible to obtain super resolved optical sections in thick samples as fast as if the sample was two‐dimensional.     

High‐resolution wide‐field microscopy with adaptive optics for spherical aberration correction and motionless focusing

Live imaging in cell biology requires three‐dimensional data acquisition with the best resolution and signal‐to‐noise ratio possible. Depth aberrations are a major source of image degradation in three‐dimensional microscopy, causing a significant loss of resolution and intensity deep into the sample. These aberrations occur because of the mismatch between the sample refractive index and the immersion medium index. We have built a wide‐field fluorescence microscope that incorporates a large‐throw deformable mirror to simultaneously focus and correct for depth aberration in three‐dimensional imaging. Imaging fluorescent beads in water and glycerol with an oil immersion lens we demonstrate a corrected point spread function and a 2‐fold improvement in signal intensity. We apply this new microscope to imaging biological samples, and show sharper images and improved deconvolution.     

Streak time-lapse video microscopy: analysis of protoplasmic motility and cell division in Tradescantia stamen hair cells

We have developed a video time-lapse analogue of a streak camera using a digital image processing technique, and have used it to analyse dynamic processes in plant cells. The same image area is selected from a succession of frames in a video tape recording. The successive images are stored in an image memory, rearranged, and displayed in a single frame according to the time course. Each image area is rectangular, with selectable length and width: the closest analogy to a streak camera is obtained when one of its sides is a single pixel. The composite image displays sequential changes in the distribution of subcellular components in the selected area. The method was shown to be useful for monitoring details of cytoplasmic streaming and organelle movement, observing the time course of chemical fixation, and also for studying kinetochore movement, shortening of chromatids and cell plate formation during mitosis and cytokinesis. Cessation and resumption of cytoplasmic movement during the cell division cycle were also clearly localized outside the nuclear region in apical cells of Tradescantia stamen hairs.     

基于快速方向预测的高分辨率遥感影像压缩

针对传统的自适应方向提升小波变换(ADL-DWT)算法在高分辨率遥感影像压缩中计算复杂度过高的问题,提出一种新的基于方向预测的提升小波变换(DP-LWT)算法,实现了高分辨率遥感影像的快速、高效压缩.新算法首先将高分辨率遥感影像分为若干不重叠子块,然后采用梯度算子快速预测遥感影像中每个图像块的最佳提升方向,并沿着最佳预测方向插值完成方向提升小波变换,最后进行多级树集合分裂(SPIHT)编码.实验结果表明,新算法有效削弱了遥感影像各子带中非水平与非垂直方向的高频系数;与传统自适应方向提升小波变换相比,在重建高分辨率遥感影像峰值信噪比基本相同的情况下,有效减少了小波变换中方向预测的计算复杂度.     

Three‐dimensional microscopy data exploration by interactive volume visualization

This paper presents a new volume visualization approach for three‐dimensional (3‐D) interactive microscopy data exploration. Because of their unique image characteristics, 3‐D microscopy data are often not able to be visualized effectively by conventional volume visualization techniques. In our approach, microscopy visualization is carried out in an interactive data exploration environment, based on a combination of interactive volume rendering techniques and image‐based transfer function design methods. Interactive volume rendering is achieved by using two‐dimensional (2‐D) texture mapping in a Shear‐Warp volume rendering algorithm. Image processing techniques are employed and integrated into the rendering pipeline for the definition and searching of appropriate transfer functions that best reflect the user's visualization intentions. These techniques have been implemented successfully in a prototype visualization system on low‐end and middle‐range SGI desktop workstations. Since only 2‐D texture mapping is required, the system can also be easily ported to PC platforms.     

Morphological enhancement of microscopy mineral image using opening‐ and closing‐based toggle operator

To enhance unclear microscopy mineral images, an algorithm based on toggle operator using opening and closing is proposed in this paper. Firstly, the specified toggle operator using opening and closing through designing the selection rules is analysed. Secondly, after importing the multiscale theory into the specified toggle operator, useful mineral image features, especially the mineral details, are extracted using the multiscale theory‐based toggle operator. Finally, the mineral image is enhanced through the strategy of enlarging the contrast between the extracted bright and dark image features. Experimental results on different types of mineral images verified that the proposed algorithm could effectively enhance mineral images and performed better than some other algorithms. The enhanced mineral image is clear and contains rich mineral details, whereas the grey scale distribution of the original mineral image is appropriately maintained. This would be useful for the further mineral analysis. Therefore, the proposed algorithm could be widely used for image‐based mineral applications.     

HisTOOLogy: an open‐source tool for quantitative analysis of histological sections

HisTOOLogy is an open‐source software for the quantification of digital colour images of histological sections. The simple graphical user interface enables both expert and non‐expert users to rapidly extract useful information from stained tissue sections. The software's main feature is a generalizable colour separation algorithm based on k‐means clustering which accurately and reproducibly returns the amount of colour per unit area for any stain, thus allowing the quantification of tissue components. Here we describe HisTOOLogy's algorithms and graphical user interface structure, showing how it can be used to separate different dye colours in several classical stains. In addition, to demonstrate how the tool can be employed to obtain quantitative information on biological tissues, the effect of different hepatic tissue decellularization protocols on cell removal and matrix preservation was assessed through image analysis using HisTOOLogy and compared with conventional DNA and total protein content assays. HisTOOLogy's performance was also compared with ImageJ's colour deconvolution plug‐in, demonstrating its advantages in terms of ease of use and speed of colour separation.     

Automatic measurement of compression wood cell attributes in fluorescence microscopy images

This paper presents a new automated method for analyzing compression wood fibers in fluorescence microscopy. Abnormal wood known as compression wood is present in almost every softwood tree harvested. Compression wood fibers show a different cell wall morphology and chemistry compared to normal wood fibers, and their mechanical and physical characteristics are considered detrimental for both construction wood and pulp and paper purposes. Currently there is the need for improved methodologies for characterization of lignin distribution in wood cell walls, such as from compression wood fibers, that will allow for a better understanding of fiber mechanical properties. Traditionally, analysis of fluorescence microscopy images of fiber cross-sections has been done manually, which is time consuming and subjective. Here, we present an automatic method, using digital image analysis, that detects and delineates softwood fibers in fluorescence microscopy images, dividing them into cell lumen, normal and highly lignified areas. It also quantifies the different areas, as well as measures cell wall thickness. The method is evaluated by comparing the automatic with a manual delineation. While the boundaries between the various fiber wall regions are detected using the automatic method with precision similar to inter and intra expert variability, the position of the boundary between lumen and the cell wall has a systematic shift that can be corrected. Our method allows for transverse structural characterization of compression wood fibers, which may allow for improved understanding of the micro-mechanical modeling of wood and pulp fibers.     

井下视频成像测井技术

井下视频成像测井利用井下摄像头获取井眼实时图像信息，可用于套管检测、落物打捞、井下作业质量检查等。文中采用基于小波变换的图像压缩技术、高速数字调制传输、基于CPLD的数字解调算法、特殊的井下仪器结构设计，解决了井下电视图像压缩，电缆高速数据传输，井下照明和保温等关键技术问题，设计出了井下电视成像测井仪样机，经过3000m电缆传输试验和125℃高温试验，仪器工作可靠、图像清晰稳定。     

Application of an advanced maximum likelihood estimation restoration method for enhanced‐resolution and contrast in second‐harmonic generation microscopy

Second‐harmonic generation (SHG) microscopy has gained popularity because of its ability to perform submicron, label‐free imaging of noncentrosymmetric biological structures, such as fibrillar collagen in the extracellular matrix environment of various organs with high contrast and specificity. Because SHG is a two‐photon coherent scattering process, it is difficult to define a point spread function (PSF) for this modality. Hence, compared to incoherent two‐photon processes like two‐photon fluorescence, it is challenging to apply the various PSF‐engineering methods to improve the spatial resolution to be close to the diffraction limit. Using a synthetic PSF and application of an advanced maximum likelihood estimation (AdvMLE) deconvolution algorithm, we demonstrate restoration of the spatial resolution in SHG images to that closer to the theoretical diffraction limit. The AdvMLE algorithm adaptively and iteratively develops a PSF for the supplied image and succeeds in improving the signal to noise ratio (SNR) for images where the SHG signals are derived from various sources such as collagen in tendon and myosin in heart sarcomere. Approximately 3.5 times improvement in SNR is observed for tissue images at depths of up to ～480 nm, which helps in revealing the underlying helical structures in collagen fibres with an ～26% improvement in the amplitude contrast in a fibre pitch. Our approach could be adapted to noisy and low resolution modalities such as micro‐nano CT and MRI, impacting precision of diagnosis and treatment of human diseases.     

一种稳健的高光谱图像压缩方法

提出了一种稳健的高光谱图像压缩技术。估计原始数据的虚拟维数,继而采用一种非监督的正交子空间投影技术提取端元矢量,构成矩阵作为快速独立分量分析的初始化混合矩阵,进行ICA变换。对变换后的独立分量图,采用二维分层树集合分裂进一步压缩编码。计算机仿真结果表明,该压缩算法在取得40∶1压缩比的同时,能有效地保持数据,尤其是小目标和异常的谱向特征,是一种高效的三维数据压缩方法,可有效地应用在小目标检测及异常检测中。     

Nano‐level position resolution for particle tracking in digital in‐line holographic microscopy

Three‐dimensional particle tracking in biological systems is a quickly growing field, many techniques have been developed providing tracking characters. Digital in‐line holographic microscopy is a valuable technique for particle tracking. However, the speckle noise, out‐of‐focus signals and twin image influenced the particle tracking. Here an adaptive noise reduction method based on bidimensional ensemble empirical mode decomposition is introduced into digital in‐line holographic microscopy. It can eliminate the speckle noise and background of the hologram adaptively. Combined with the three‐dimensional deconvolution approach in the reconstruction, the particle feature would be identified effectively. Tracking the fixed beads on the cover‐glass with piezoelectric stage through multiple holographic images demonstrate the tracking resolution, which approaches 2 nm in axial direction and 1 nm in transverse direction. This would facilitate the development and use in the biological area such as living cells and single‐molecule approaches.     

一种超光谱图像分层压缩方法

根据超光谱图像有很强谱间相关性的成像特点,设计了一种预测算法结合变换编码算法的图像分层压缩方法。采用几个相邻波段图像共享同一有损图像作为预测图像,克服了预测算法对传输误差的敏感性。预测图像是通过对原始图像进行局部熵为代价函数的四叉树分割后,再经小波变换得到的。用各个原始图像减去共享预测图像来去除谱间相关性,并得到相应残差图像,再对残差图像采用局部离散余弦基变换方法去除空间相关性,实现近无损压缩。研究结果表明,各波段峰值信噪比(PSNR)为40dB左右时,压缩比(CR)高于7.2,分层压缩方法具有很好的压缩效果。     

基于EBCOT的平衡多小波航空图像压缩编码

鉴于预滤波有可能造成多小波的正交性、对称性的"丢失"及基函数支撑的增加,提出了多小波"平衡"算法,使得多小波基有与单小波基相同的性质。充分利用平衡多小波分解系数的结构,采用EBCOT图像编码算法,对平衡多小波系数进行压缩处理。当压缩比为32时,峰值信号比为31.342 7。实验结果表明:基于EBCOT的平衡多小波算法同时具有图像压缩所需要的正交性、对称性、短支撑和较大的消失矩等多个良好特性, 是一种比较有效的航空图像压缩方法。     

基于车载多媒体视音系统中图片压缩解压缩算法的研究

对计算机屏幕图像的压缩一般是直接用传统的RLE、LZW或JPEG算法.以上算法对微控制器系统中图片压缩难以达到压缩比和压缩速度的兼顾.本文提出了一种多级分块压缩算法.首先将屏幕图片分成复杂图形块和简单图形块.然后对简单块采用无失真压缩算法.对复杂块采用有失真压缩算法压缩.解压缩时对不同的块分别用逆压缩算法进行解压缩,最后再把各个块复合成一副图片.试验证明,本文所提出的压缩算法对车载多媒体视音系统中图片压缩比较大,压缩和解压缩速度快,性能优于传统的压缩算法.     

An overview of state‐of‐the‐art image restoration in electron microscopy

In Life Science research, electron microscopy (EM) is an essential tool for morphological analysis at the subcellular level as it allows for visualization at nanometer resolution. However, electron micrographs contain image degradations such as noise and blur caused by electromagnetic interference, electron counting errors, magnetic lens imperfections, electron diffraction, etc. These imperfections in raw image quality are inevitable and hamper subsequent image analysis and visualization. In an effort to mitigate these artefacts, many electron microscopy image restoration algorithms have been proposed in the last years. Most of these methods rely on generic assumptions on the image or degradations and are therefore outperformed by advanced methods that are based on more accurate models. Ideally, a method will accurately model the specific degradations that fit the physical acquisition settings. In this overview paper, we discuss different electron microscopy image degradation solutions and demonstrate that dedicated artefact regularisation results in higher quality restoration and is applicable through recently developed probabilistic methods.     

Semi-automated measurement of true chord length distributions and moments by video microscopy and image analysis

The distribution of the lengths of airspace chords in pulmonary parenchyma characterizes many architectural features of the alveoli and alveolar ducts. Laborious to obtain manually, the distributions and density functions may be acquired semi-automatically by video microscopy, digitization and image processing. The accuracy of the estimation is influenced by the microscopical methods and also by the techniques used (i) to convert the digitized grey-scale picture to a two-valued image, (ii) to collect the chord lengths and (iii) to compensate for finite field widths. The last problem arises because some chords are completely visible within a field while others are only partially seen, since one of the two air-tissue boundaries lies outside the field of view. This error systematically biases the observed distribution. This paper contains solutions to hardware, software and analytic problems encountered while developing the capability to measure airspace chord length density functions semi-automatically. Formulas for estimating the true chord length density function from samples of observed chord lengths are presented. Also given are formulas for the estimation of the first and second moments of the true chord length distribution from the means of observed chord lengths. These techniques of image preparation and analysis should be suitable for characterizing particle, grain or cell size distributions, especially where many profiles fall partially outside the field of view.