Selected annotated instance segmentation sub-volumes from a large scale CT data-set of a historic aircraft.

The Me 163 was a Second World War fighter airplane and is currently displayed in the Deutsches Museum in Munich, Germany. A complete computed tomography (CT) scan was obtained using a large scale industrial CT scanner to gain insights into its history, design, and state of preservation. The CT data enables visual examination of the airplane's structural details across multiple scales, from the entire fuselage to individual sprockets and rivets. However, further processing requires instance segmentation of the CT data-set. Currently, there are no adequate computer-assisted tools for automated or semi-automated segmentation of such large scale CT airplane data. As a first step, an interactive data annotation process has been established. So far, seven 512 × 512 × 512 voxel sub-volumes of the Me 163 airplane have been annotated, which can potentially be used for various applications in digital heritage, non-destructive testing, or machine learning. This work describes the data acquisition process, outlines the interactive segmentation and post-processing, and discusses the challenges associated with interpreting and handling the annotated data.

Radioactivity and GMO-Free Sterile Insect Technology for the Sustainable Control of the Invasive Pest Drosophila suzukii.

Drosophila suzukii (D. suzukii), commonly known as the spotted wing drosophila, is a highly invasive crop pest that is difficult to control using chemical insecticides. To address the urgent need for alternative and more sustainable control strategies, the sterile insect technique (SIT) is improved, which involves the release of sterilized male insects to mate with fertile conspecifics, thereby reducing the size of the pest population in the subsequent generation. The three critical aspects that influence the success of SIT programs in D. suzukii are addressed. First, an accurate and nondestructive method is established to determine the sex of individual insects based on the differential weight of male and female pupae. Second, conditions for X-ray sterilization are systematically tested and an optimal dose (90 kV/40 Gy) is identified that ensures the efficient production of sterile D. suzukii for release. Finally, the inherent thermosensitivity of D. suzukii males is exploited to develop a temperature-based sterilization technique, offering an alternative or additional SIT method for this pest. These advances will contribute to the development of a comprehensive and effective strategy for the management of D. suzukii populations, reducing their impact on agriculture and helping to safeguard crop yields.

3D segmentation of plant root systems using spatial pyramid pooling and locally adaptive field-of-view inference.

Background: The non-invasive 3D-imaging and successive 3D-segmentation of plant root systems has gained interest within fundamental plant research and selectively breeding resilient crops. Currently the state of the art consists of computed tomography (CT) scans and reconstruction followed by an adequate 3D-segmentation process. Challenge: Generating an exact 3D-segmentation of the roots becomes challenging due to inhomogeneous soil composition, as well as high scale variance in the root structures themselves. Approach: (1) We address the challenge by combining deep convolutional neural networks (DCNNs) with a weakly supervised learning paradigm. Furthermore, (2) we apply a spatial pyramid pooling (SPP) layer to cope with the scale variance of roots. (3) We generate a fine-tuned training data set with a specialized sub-labeling technique. (4) Finally, to yield fast and high-quality segmentations, we propose a specialized iterative inference algorithm, which locally adapts the field of view (FoV) for the network. Experiments: We compare our segmentation results against an analytical reference algorithm for root segmentation (RootForce) on a set of roots from Cassava plants and show qualitatively that an increased amount of root voxels and root branches can be segmented. Results: Our findings show that with the proposed DCNN approach combined with the dynamic inference, much more, and especially fine, root structures can be detected than with a classical analytical reference method. Conclusion: We show that the application of the proposed DCNN approach leads to better and more robust root segmentation, especially for very small and thin roots.

"Chamber #8" - a holistic approach of high-throughput non-destructive assessment of plant roots.

Introduction: In the past years, it has been observed that the breeding of plants has become more challenging, as the visible difference in phenotypic data is much smaller than decades ago. With the ongoing climate change, it is necessary to breed crops that can cope with shifting climatic conditions. To select good breeding candidates for the future, phenotypic experiments can be conducted under climate-controlled conditions. Above-ground traits can be assessed with different optical sensors, but for the root growth, access to non-destructively measured traits is much more challenging. Even though MRI or CT imaging techniques have been established in the past years, they rely on an adequate infrastructure for the automatic handling of the pots as well as the controlled climate. Methods: To address both challenges simultaneously, the non-destructive imaging of plant roots combined with a highly automated and standardized mid-throughput approach, we developed a workflow and an integrated scanning facility to study root growth. Our "chamber #8" contains a climate chamber, a material flow control, an irrigation system, an X-ray system, a database for automatic data collection, and post-processing. The goals of this approach are to reduce the human interaction with the various components of the facility to a minimum on one hand, and to automate and standardize the complete process from plant care via measurements to root trait calculation on the other. The user receives standardized phenotypic traits and properties that were collected objectively. Results: The proposed holistic approach allows us to study root growth of plants in a field-like substrate non-destructively over a defined period and to calculate phenotypic traits of root architecture. For different crops, genotypic differences can be observed in response to climatic conditions which have already been applied to a wide variety of root structures, such as potatoes, cassava, or corn. Discussion: It enables breeders and scientists non-destructive access to root traits. Additionally, due to the non-destructive nature of X-ray computed tomography, the analysis of time series for root growing experiments is possible and enables the observation of kinetic traits. Furthermore, using this automation scheme for simultaneously controlled plant breeding and non-destructive testing reduces the involvement of human resources.

X-ray driven peanut trait estimation: computer vision aided agri-system transformation.

BACKGROUND: In India, raw peanuts are obtained by aggregators from smallholder farms in the form of whole pods and the price is based on a manual estimation of basic peanut pod and kernel characteristics. These methods of raw produce evaluation are slow and can result in procurement irregularities. The procurement delays combined with the lack of storage facilities lead to fungal contaminations and pose a serious threat to food safety in many regions. To address this gap, we investigated whether X-ray technology could be used for the rapid assessment of the key peanut qualities that are important for price estimation. RESULTS: We generated 1752 individual peanut pod 2D X-ray projections using a computed tomography (CT) system (CTportable160.90). Out of these projections we predicted the kernel weight and shell weight, which are important indicators of the produce price. Two methods for the feature prediction were tested: (i) X-ray image transformation (XRT) and (ii) a trained convolutional neural network (CNN). The prediction power of these methods was tested against the gravimetric measurements of kernel weight and shell weight in diverse peanut pod varieties1. Both methods predicted the kernel mass with R2 > 0.93 (XRT: R2 = 0.93 and mean error estimate (MAE) = 0.17, CNN: R2 = 0.95 and MAE = 0.14). While the shell weight was predicted more accurately by CNN (R2 = 0.91, MAE = 0.09) compared to XRT (R2 = 0.78; MAE = 0.08). CONCLUSION: Our study demonstrated that the X-ray based system is a relevant technology option for the estimation of key peanut produce indicators (Figure 1). The obtained results justify further research to adapt the existing X-ray system for the rapid, accurate and objective peanut procurement process. Fast and accurate estimates of produce value are a necessary pre-requisite to avoid post-harvest losses due to fungal contamination and, at the same time, allow the fair payment to farmers. Additionally, the same technology could also assist crop improvement programs in selecting and developing peanut cultivars with enhanced economic value in a high-throughput manner by skipping the shelling of the pods completely. This study demonstrated the technical feasibility of the approach and is a first step to realize a technology-driven peanut production system transformation of the future.

Set up from the beginning: The origin and early development of cassava storage roots.

Despite the importance of storage root (SR) organs for cassava and the other root crops yield, their developmental origin is poorly understood. Here we use multiple approaches to shed light on the initial stages of root development demonstrating that SR and fibrous roots (FR) follow different rhizogenic processes. Transcriptome analysis carried out on roots collected before, during and after root bulking highlighted early and specific activation of a number of functions essential for root swelling and identified root-specific genes able to effectively discriminate emerging FR and SR. Starch and sugars start to accumulate at a higher rate in SR before they swell but only after parenchyma tissue has been produced. Finally, using non-destructive computed tomography measurements, we show that SR (but not FR) contain, since their emergence from the stem, an inner channel structure in continuity with the stem secondary xylem, indicating that SR derive from a distinct rhizogenic process compared with FR.

X-Ray CT Phenotyping Reveals Bi-Phasic Growth Phases of Potato Tubers Exposed to Combined Abiotic Stress.

As a consequence of climate change, heat waves in combination with extended drought periods will be an increasing threat to crop yield. Therefore, breeding stress tolerant crop plants is an urgent need. Breeding for stress tolerance has benefited from large scale phenotyping, enabling non-invasive, continuous monitoring of plant growth. In case of potato, this is compromised by the fact that tubers grow belowground, making phenotyping of tuber development a challenging task. To determine the growth dynamics of tubers before, during and after stress treatment is nearly impossible with traditional destructive harvesting approaches. In contrast, X-ray Computed Tomography (CT) offers the opportunity to access belowground growth processes. In this study, potato tuber development from initiation until harvest was monitored by CT analysis for five different genotypes under stress conditions. Tuber growth was monitored three times per week via CT analysis. Stress treatment was started when all plants exhibited detectable tubers. Combined heat and drought stress was applied by increasing growth temperature for 2 weeks and simultaneously decreasing daily water supply. CT analysis revealed that tuber growth is inhibited under stress within a week and can resume after the stress has been terminated. After cessation of stress, tubers started growing again and were only slightly and insignificantly smaller than control tubers at the end of the experimental period. These growth characteristics were accompanied by corresponding changes in gene expression and activity of enzymes relevant for starch metabolism which is the driving force for tuber growth. Gene expression and activity of Sucrose Synthase (SuSy) reaffirmed the detrimental impact of the stress on starch biosynthesis. Perception of the stress treatment by the tubers was confirmed by gene expression analysis of potential stress marker genes whose applicability for potato tubers is further discussed. We established a semi-automatic imaging pipeline to analyze potato tuber delevopment in a medium thoughput (5 min per pot). The imaging pipeline presented here can be scaled up to be used in high-throughput phenotyping systems. However, the combination with automated data processing is the key to generate objective data accelerating breeding efforts to improve abiotic stress tolerance of potato genotypes.

Semiautomated 3D Root Segmentation and Evaluation Based on X-Ray CT Imagery.

BACKGROUND: Computed X-ray tomography (CTX) is a high-end nondestructive approach for the visual assessment of root architecture in soil. Nevertheless, in order to evaluate high-resolution CTX data of root architectures, manual segmentation of the depicted root systems from large-scale volume data is currently necessary, which is both time consuming and error prone. The duration of such a segmentation is of importance, especially for time-resolved growth analysis, where several instances of a plant need to be segmented and evaluated. Specifically, in our application, the contrast between soil and root data varies due to different growth stages and watering situations at the time of scanning. Additionally, the root system itself is expanding in length and in the diameter of individual roots. OBJECTIVE: For semiautomated and robust root system segmentation from CTX data, we propose the RootForce approach, which is an extension of Frangi's "multi-scale vesselness" method and integrates a 3D local variance. It allows a precise delineation of roots with diameters down to several µm in pots with varying diameters. Additionally, RootForce is not limited to the segmentation of small below-ground organs, but is also able to handle storage roots with a diameter larger than 40 voxels. RESULTS: Using CTX volume data of full-grown bean plants as well as time-resolved (3D + time) growth studies of cassava plants, RootForce produces similar (and much faster) results compared to manual segmentation of the regarded root architectures. Furthermore, RootForce enables the user to obtain traits not possible to be calculated before, such as total root volume (V root), total root length (L root), root volume over depth, root growth angles (θ min, θ mean, and θ max), root surrounding soil density D soil, or form fraction F. Discussion. The proposed RootForce tool can provide a higher efficiency for the semiautomatic high-throughput assessment of the root architectures of different types of plants from large-scale CTX. Furthermore, for all datasets within a growth experiment, only a single set of parameters is needed. Thus, the proposed tool can be used for a wide range of growth experiments in the field of plant phenotyping.

Migrating Shear Bands in Shaken Granular Matter.

When dense granular matter is sheared, the strain is often localized in shear bands. After some initial transient these shear bands become stationary. Here, we introduce a setup that periodically creates horizontally aligned shear bands which then migrate upward through the sample. Using x-ray radiography we demonstrate that this effect is caused by dilatancy, the reduction in volume fraction occurring in sheared dense granular media. Further on, we argue that these migrating shear bands are responsible for the previously reported periodic inflating and collapsing of the material.

Drought and heat stress tolerance screening in wheat using computed tomography.

BACKGROUND: Improving abiotic stress tolerance in wheat requires large scale screening of yield components such as seed weight, seed number and single seed weight, all of which is very laborious, and a detailed analysis of seed morphology is time-consuming and visually often impossible. Computed tomography offers the opportunity for much faster and more accurate assessment of yield components. RESULTS: An X-ray computed tomographic analysis was carried out on 203 very diverse wheat accessions which have been exposed to either drought or combined drought and heat stress. Results demonstrated that our computed tomography pipeline was capable of evaluating grain set with an accuracy of 95-99%. Most accessions exposed to combined drought and heat stress developed smaller, shrivelled seeds with an increased seed surface. As expected, seed weight and seed number per ear as well as single seed size were significantly reduced under combined drought and heat compared to drought alone. Seed weight along the ear was significantly reduced at the top and bottom of the wheat spike. CONCLUSIONS: We were able to establish a pipeline with a higher throughput with scanning times of 7 min per ear and accuracy than previous pipelines predicting a set of agronomical important seed traits and to visualize even more complex traits such as seed deformations. The pipeline presented here could be scaled up to use for high throughput, high resolution phenotyping of tens of thousands of heads, greatly accelerating breeding efforts to improve abiotic stress tolerance.

Direct comparison of MRI and X-ray CT technologies for 3D imaging of root systems in soil: potential and challenges for root trait quantification.

BACKGROUND: Roots are vital to plants for soil exploration and uptake of water and nutrients. Root performance is critical for growth and yield of plants, in particular when resources are limited. Since roots develop in strong interaction with the soil matrix, tools are required that can visualize and quantify root growth in opaque soil at best in 3D. Two modalities that are suited for such investigations are X-ray Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Due to the different physical principles they are based on, these modalities have their specific potentials and challenges for root phenotyping. We compared the two methods by imaging the same root systems grown in 3 different pot sizes with inner diameters of 34 mm, 56 mm or 81 mm. RESULTS: Both methods successfully visualized roots of two weeks old bean plants in all three pot sizes. Similar root images and almost the same root length were obtained for roots grown in the small pot, while more root details showed up in the CT images compared to MRI. For the medium sized pot, MRI showed more roots and higher root lengths whereas at some spots thin roots were only found by CT and the high water content apparently affected CT more than MRI. For the large pot, MRI detected much more roots including some laterals than CT. CONCLUSIONS: Both techniques performed equally well for pots with small diameters which are best suited to monitor root development of seedlings. To investigate specific root details or finely graduated root diameters of thin roots, CT was advantageous as it provided the higher spatial resolution. For larger pot diameters, MRI delivered higher fractions of the root systems than CT, most likely because of the strong root-to-soil contrast achievable by MRI. Since complementary information can be gathered with CT and MRI, a combination of the two modalities could open a whole range of additional possibilities like analysis of root system traits in different soil structures or under varying soil moisture.

Temperature dependent cubic and hexagonal close packing in micellar structures.

The interfacial structure and phase diagram of a micellar solution formed by the three block copolymer (EO20-PO70-EO20) also known as P123 solved in deuterated water close to a solid boundary is investigated with respect to temperature. We find a hysteretic behavior of the d-spacing of the micellar crystal and a spontaneous change in the lateral correlation length going hand in hand with a structural reorganization between cubic and hexagonal. The phase transitions may be initiated by a change in the shape of the micelles from spherical to elongated together with a minimization of the polymer water interface.

Depletion at solid/liquid interfaces: flowing hexadecane on functionalized surfaces.

We present a neutron reflectivity study on interfaces in contact with flowing hexadecane, which is known to exhibit surface slip on functionalized solid surfaces. The single crystalline silicon substrates were either chemically cleaned Si(100) or Si(100) coated by octadecyl-trichlorosilane (OTS), which resulted in different interfacial energies. The liquid was sheared in situ and changes in reflectivity profiles were compared to the static case. For the OTS surface, the temperature dependence was also recorded. For both types of interfaces, density depletion of the liquid at the interface was observed. In the case of the bare Si substrate, shear load altered the structure of the depletion layer, whereas for the OTS covered surface no effect of shear was observed. Possible links between the depletion layer and surface slip are discussed. The results show that, in contrast to water, for hexadecane the enhancement of the depletion layer with temperature and interfacial energy reduces the amount of slip. Thus a density depletion cannot be the origin of surface slip in this system.

Shear induced relaxation of polymer micelles at the solid-liquid interface.

A 20% aqueous solution of (ethylene oxide) 99-(propylene oxide) 65-(ethylene oxide) 99, F127, was investigated by combining rheology in a cone/plate-geometry and surface-sensitive grazing incident neutron scattering. The crystalline structure formed by the polymer micelles becomes less pronounced for low shear rates, but correlations increase for higher shear rates. After stopping shear a slow relaxation of the micelles is found in the vicinity (50 mum thick layer) of a hydrophilic silicon wall (strong micelle-wall interaction), while a fast relaxation is observed in the boundary layer against the hydrophobic silicon wall (weak micelle-wall interaction). The results show that in the vicinity of the interface wall-particle interactions compete heavily with the shear force acting on the liquid.