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There are two different styles of file formats available in VTK. The simplest are the legacy, serial formats that are easy to read and write either by hand or programmatically. However, these formats are less flexible than the XML based file formats described later in this section. The XML formats support random access, parallel I/O, and portable data compression and are preferred to the serial VTK file formats whenever possible.
Binary files in VTK are portable across different computer systems as long as you observe two conditions. First, make sure that the byte ordering of the data is correct, and second, make sure that the length of each data type is consistent.
VTK provides another set of data formats using XML syntax. While these formats are much more complicated than the original VTK format described previously (see Simple Legacy Formats), they support many more features. The major motivation for their development was to facilitate data streaming and parallel I/O. Some features of the format include support for compression, portable binary encoding, random access, big endian and little endian byte order, multiple file representation of piece data, and new file extensions for different VTK dataset types. XML provides many features as well, especially the ability to extend a file format with application specific tags.
With the global increase in food demand, selecting crops that perform well is critical to improving food production. Breeding for better crops includes selecting desirable phenotypic traits. However, isolating plants with particular phenotypes accurately and nondestructively is still challenging because it involves analyzing hundreds to thousands of samples and sometimes selecting specific complex features at multiscale levels ranging from the cell, tissue, and organ to the whole plant [1, 2]. Many platforms are available to achieve multimodal and multidimensional phenotyping. These platforms can operate in a wide range of conditions ranging from controlled and semi-controlled environments to field conditions [2, 3]. High-throughput phenotyping is performed primarily at the organism and organ levels and has a limited resolution. Examples of these platforms include PlantScreenTM Systems, equipped with a three-dimensional (3D) laser and multispectral camera and have a range of instruments that allow phenotyping in growth chambers, greenhouses, and the field.Footnote 1 Some systems can also phenotype the roots grown in either RhizotronsFootnote 2 [4] or RhizotubesFootnote 3 [5]. The PlantEye can automatically image and compute multiple above-ground features nondestructivelyFootnote 4 [6]. Other platforms are tailored to more specific traits, such as Phenopsis, which monitors the plant response to a water deficit [7]. In addition, LiDAR is a creative system for high-throughput phenotyping in the field [8, 9]. Additional platforms have also been valuable for live imaging. The 3D root growth and imaging system allows high-throughput phenotyping of rice root traits at the seedling stage [10]. RhizoChamber is a robotic platform used to analyze root growth in rhizoboxes [11]. The system integrates hardware and software to analyze the spatio-temporal dynamics of root growth from time-course images of multiple plants. Although these systems allow high-throughput phenotyping, they are costly. Another attractive system to monitor root growth noninvasively is X-ray Computed Tomography, which allows 3D root phenotyping in soil [12]. However, the system does not allow high-throughput phenotyping, the resolution is low and is also costly. Recently, efforts have been put forward to establish alternative approaches for low-cost live imaging of plants under stress conditions [13, 14]. For higher magnification imaging, the most commonly used systems are costly stereomicroscopes coupled with digital cameras. The proposed hybrid mini-microscope offers an alternative low-cost tool that combines physical and optical magnification to achieve high magnification and multifluorescence imaging [15, 16]. Although some of these platforms are easy to operate, and images can be captured rapidly, they are often heavy and nonportable, and the setup is inflexible. Moreover, they allow only one mode of imaging. High-throughput phenotyping often comes at the expense of resolution, whereas phenotyping at a high spatial and temporal resolution is difficult to achieve at large scales.
This study proposes a platform that combines high-throughput phenotyping with high resolution. The platform can be used as a single-plate system to monitor biological processes at a high resolution. MultipleXLab is an optical, modular imaging setup for high-throughput phenotyping of seed germination and early root growth on agar and soil plates. MultipleXLab is based on off-the-shelf, low-cost, portable camera components that we modified and adapted to capture dynamic processes noninvasively in living biological systems. The system comprises a digital camera and two different types of 3D-printed multiplate holders with integrated growth LED lighting. Users can simultaneously capture 18 square Petri dish plates containing multiple specimens, allowing screening of up to thousands of Arabidopsis seedlings to monitor germination rates and root-growth dynamics noninvasively. The system can acquire and analyze up to 100 images per hour, with each image having up to 64 seeds or roots, which allows automated imaging of thousands of Arabidopsis and hundreds of tomato seedlings growing on agar plates at a high resolution. We also implemented computer-vision and pattern recognition technologies combined with machine learning to analyze and quantify distinct phenotypes. We used MultipleXLab to determine differences in seed germination index and growth rates of developmental, auxin, and cell-cycle mutants.
With this setup, we detected microscopic worms and free-living nematodes interacting with the tomato root surface in the soil (Additional file 4: Movie S3) and insects feeding off the surface of a tomato root (Additional file 5: Movie S4). Because the system is portable, we tested its long-term capabilities outside the laboratory by placing it in the greenhouse and monitoring root recovery after wounding using tomato plants (Additional file 1: Fig. S2, A to J). Our live time-lapse imaging system allowed us to determine the recovery time for roots after wounding and monitor the root regeneration process occurring after 45 to 50 hours in cut roots (Additional file 1: Fig. S2G and Additional file 6: Movie S5).
The iron (Fe) was the most abundant element at the subway stations including this study. A previous study on subway particles indicated that Fe-containing particles were the most common subway particle by weight concentration. Most Fe/Si-rich particles were found in the subway particle samples obtained by the portable collectors in London, accounting for 53 percent of the overall particles65. The iron concentrations of New York, Helsinki, Tokyo, and Budapest ranged from 40 to 92%66,67,68,69.
This paper discusses results obtained from in situ analysis of the tesserae of the Roman mosaic of Los Amores (Cástulo site, Linares, Spain) dating back to the turn of the 1st to the 2nd century AD. Specifically, it focuses on the scene The Judgment of Paris. In view of the exceptional state of preservation of the mosaic, from which very few tesserae had fallen off, non-invasive methods with portable Micro Raman Spectroscopy (MRS) and hand-held X-ray fluorescence (hXRF) and data assessment by use of principal component analysis and binary representations were selected. The results obtained allow to evaluate both the analytical method and the portable equipment used, as well as to classify the raw materials, the colouring agents and the opacifiers used. MRS analysis proved crucial for the identification of stone tesserae (ironstones, carbonate and siliciclastic rocks) and for the identification of the type of glasses used (soda-lime-silicate and lead type glasses) based on the analysis of two detached tesserae. hXRF analysis of the glass tesserae identified both colouring agents (Co, Cu, Pb, Zn) and opacifiers (calcium antimonate). The data obtained lend themselves to an assessment of the degradation process that threaten the integrity of the mosaic. The identification of tessera made of specific stone materials (especially ironstone) and of lead glass tesserae suggest the existence of a mosaic workshop in the Upper Guadalquivir (Eastern Andalusia, Spain).
The methodological dimension of the second objective was aimed at exploring the capacity and enhancing the use of portable equipment in the in-situ analysis of mosaics. Given the undesirability of disturbing them by removing a significant repertory of the tesserae for study, non-invasive strategies need to be developed to analyse them in situ. Thus, this proposal comprises the use of portable equipment able to carry out readings of the mineral (portable MRS) and elemental (handheld XRF) compositions. A joint analysis undertaken with both techniques allows us to analyse both stone and glass tesserae with greater guarantees.
The spectroscopic techniques selected have been used frequently and successfully on Roman mosaic tesserae from all over the Mediterranean, although in those cases by analysing separate tesserae with high precision laboratory equipment [19,20,21,22,23]. In contrast, the combined application of portable equipment to analyse mosaics has so far been infrequent [24,25,26]. Nevertheless, it is necessary because in many cases it is the only option for undertaking a comprehensive study of a mosaic. Los Amores Mosaic is an excellent example of this situation. Our investigation also had the advantage of preliminary studies in which the effectiveness of various types of portable Raman and hXRF equipment were tested, with the specific portable devices used showing good applicability and performance [27, 28]. 2ff7e9595c
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