The determination of optimum segmentation parameters using genetic algorithms: Application to different segmentation algorithms and transmission electron microscopy tomography reconstructed volumes

A method for optimizing an automatic selection of values for parameters that feed segmentation algorithms is proposed. Evolutionary optimization techniques in combination with a fitness function based on a mutual information parameter have been used to find the optimal parameter values of region growing, fuzzy c-means and graph cut segmentation algorithms. To validate the method, the segmentation of two transmission electron microscopy tomography reconstructed volumes of a carbon black-reinforced rubber and a polylactic acid and clay nanocomposite is carried out (i) using evolutionary optimization techniques and (ii) manually by experts. The results confirm that the use of evolutionary optimization techniques, such as genetic algorithms, reduces the computational operation cost needed for a total grid search of segmentation parameters, reducing the probability of reaching a false optimum, and improving the segmentation quality. HIGHLIGHTS: A new approach to optimize 3D segmentation algorithms. Methodology to optimize segmentation parameters and improve segmentation quality. Improvement on the results when using region growing, fuzzy c-means and graph cuts algorithms.

New Perspectives for Evaluating the Mass Transport in Porous Catalysts and Unfolding Macro- and Microkinetics

In this article we shed light on newly emerging perspectives to characterize and understand the interplay of diffusive mass transport and surface catalytic processes in pores of gas phase metal catalysts. As a case study, nanoporous gold, as an interesting example exhibiting a well-defined pore structure and a high activity for total and partial oxidation reactions is considered. PFG NMR (pulsed field gradient nuclear magnetic resonance) measurements allowed here for a quantitative evaluation of gas diffusivities within the material. STEM (scanning transmission electron microscopy) tomography furthermore provided additional insight into the structural details of the pore system, helping to judge which of its features are most decisive for slowing down mass transport. Based on the quantitative knowledge about the diffusion coefficients inside a porous catalyst, it becomes possible to disentangle mass transport contributions form the measured reaction kinetics and to determine the kinetic rate constant of the underlying catalytic surface reaction. In addition, predictions can be made for an improved effectiveness of the catalyst, i.e., optimized conversion rates. This approach will be discussed at the example of low-temperature CO oxidation, efficiently catalysed by npAu at 30 °C. The case study shall reveal that novel porous materials exhibiting well-defined micro- and mesoscopic features and sufficient catalytic activity, in combination with modern techniques to evaluate diffusive transport, offer interesting new opportunities for an integral understanding of catalytic processes.

Graphical Abstract

Three-dimensional Architecture of Cyrilia lignieresi Gametocyte-stage Development Inside Red Blood Cells

The Haemogregarinidae family (Apicomplexa: Adeleina) comprises hemoprotozoa that infect mammals, birds, amphibians, fish and reptiles. Some morphological characteristics of the Cyrilia lignieresi have been described previously, but the parasite-erythrocyte relationship is still poorly understood. In order to understand the structural architecture of Cyrilia lignieresi-infected red blood cells, electron microscopy-based three-dimensional reconstruction was carried out using TEM as well as FIB-SEM tomography. Results showed that development of the macrogametocyte-stage inside the red blood cell is related to an increase in cleft-like structures in the host cell cytoplasm. Furthermore, other aspects related to parasite intraerythrocytic development were explored by 3D visualization techniques. We observed the invagination of a large extension of the Inner Membrane Complex on the parasite body, which results from or induces a folding of the posterior end of the parasite. Small tubular structures were seen associated with areas related to Inner Membrane Complex folding. Taken together, results provide new information on the remodeling of erythrocytes induced by the protozoan C. lignieresi.

Understanding and Controlling the Crystallization Process in Reconfigurable Plasmonic Superlattices

The crystallization of nanomaterials is a primary source of solid-state, photonic structures. Thus, a detailed understanding of this process is of paramount importance for the successful application of photonic nanomaterials in emerging optoelectronic technologies. While colloidal crystallization has been thoroughly studied, for example, with advanced in situ electron microscopy methods, the noncolloidal crystallization (freezing) of nanoparticles (NPs) remains so far unexplored. To fill this gap, in this work, we present proof-of-principle experiments decoding a crystallization of reconfigurable assemblies of NPs at a solid state. The chosen material corresponds to an excellent testing bed, as it enables both in situ and ex situ investigation using X-ray diffraction (XRD), transmission electron microscopy (TEM), high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), atomic force microscopy (AFM), and optical spectroscopy in visible and ultraviolet range (UV-vis) techniques. In particular, ensemble measurements with small-angle XRD highlighted the dependence of the correlation length in the NPs assemblies on the number of heating/cooling cycles and the rate of cooling. Ex situ TEM imaging further supported these results by revealing a dependence of domain size and structure on the sample preparation route and by showing we can control the domain size over 2 orders of magnitude. The application of HAADF-STEM tomography, combined with in situ thermal control, provided three-dimensional single-particle level information on the positional order evolution within assemblies. This combination of real and reciprocal space provides insightful information on the anisotropic, reversibly reconfigurable assemblies of NPs. TEM measurements also highlighted the importance of interfaces in the polydomain structure of nanoparticle solids, allowing us to understand experimentally observed differences in UV-vis extinction spectra of the differently prepared crystallites. Overall, the obtained results show that the combination of in situ heating HAADF-STEM tomography with XRD and ex situ TEM techniques is a powerful approach to study nanoparticle freezing processes and to reveal the crucial impact of disorder in the solid-state aggregates of NPs on their plasmonic properties.

Dendroids, Discrete Covalently Cross-Linked Dendrimer Superstructures

A versatile method is presented to form dendrimer superstructures by exploiting coacervate-core micelles as a template to confine and organize the hyperbranched macromolecules. First, complex coacervate-core micelles are formed from negative-neutral block copolymers and positively charged polyamidoamine dendrimers. The dendrimers inside the micellar core are then covalently cross-linked with each other upon addition of glutaraldehyde. After removal of the block copolymer from the assembly by increasing the salt concentration, consecutively, the formed Schiff bases cross-linking the dendrimers are reduced to amines, followed by a final dialysis step. This leads to well-defined covalently cross-linked nanostructures, coined dendroids, with a size of around 30 nm in diameter and a molecular weight of approximately 2.5 MDa. By incorporating dendrimer-encapsulated gold nanoparticles (AuDENs) into the micelle template strategy, the aggregation number of dendrimers inside the dendroids is determined by counting the nanoparticles in TEM micrographs. Furthermore, TEM performed at different tilt angles and AFM analysis corroborate formation of stable, covalently linked three-dimensional structures. Reconstruction of the TEM tilt series results in a tomogram further illustrating the 3D distribution of the gold nanoparticles, and hence the individual dendrimers, in the nanostructure. These dendroids appear to have a hard, poorly compressible core and a relatively soft outside. The versatility of the hierarchical building up of the supermolecules is illustrated by the controlled and synchronous incorporation of empty dendrimers and AuDENs into a single hybrid dendroid structure. The presented strategy allows for the preparation of a variety of classes of supermolecules, depending on the type of micellar-core macromolecule, e.g., dendrimer, cross-linker, and nanoparticles, used. Considering the broad interest in dendrimers as well as micelles in a plethora of research areas, e.g., (targeted) drug delivery, biomedical imaging, theragnostics, and catalysis, there is a great potential for dendroids and related classes of covalently linked macromolecules, viz., supermolecules.

Viburnum tinus Fruits Use Lipids to Produce Metallic Blue Structural Color

Viburnum tinus is an evergreen shrub that is native to the Mediterranean region but cultivated widely in Europe and around the world. It produces ripe metallic blue fruits throughout winter [1]. Despite its limited fleshy pulp [2], its high lipid content [3] makes it a valuable resource to the small birds [4] that act as its seed-dispersers [5]. Here, we find that the metallic blue appearance of the fruits is produced by globular lipid inclusions arranged in a disordered multilayer structure. This structure is embedded in the cell walls of the epicarp and underlaid with a dark layer of anthocyanin pigments. The presence of such large, organized lipid aggregates in plant cell walls represents a new mechanism for structural coloration and may serve as an honest signal of nutritional content.

In Situ Eco Encapsulation of Bioactive Agrochemicals within Fully Organic Nanotubes

Agrochemical encapsulation agents used up to now are commonly based on polymeric compounds or metal particles, but the employment of other natural products such as host structures has not been tackled in detail. In the work reported here, fully organic nanotubes composed of human bile acid (lithocholic acid) have been synthesized. These nanotubes were employed to encapsulate potential disulfide herbicide mimics that have previously shown relevant inhibitory activity against weeds. The three-dimensional chemical information from scanning transmission electron microscope analytical tomography with subnanometer scale resolution convincingly demonstrates for the first time the occurrence of efficient encapsulation within a fully organic nanotube of different organic molecules with activity as herbicides. The encapsulation was achieved in a one-pot synthesis, in an aqueous environment and under in situ conditions without using any marker or coating with contrast materials, which renders the process greener than those routinely used. The nanotubes allow complete water solubilization, with an encapsulation percentage of up to 78% in all of the herbicide compounds. Furthermore, nanotubes showed a flattened arrangement due to the host-guest interaction. The synthetic approach represents a step forward in solving the key problem of the quite limited solubility of natural agrochemicals in aqueous environments. In addition, the process presents a breakthrough in the use of natural products produced by the human body as encapsulating agents, which expands possible future applications. The preliminary docking approach clarifies that the 2o01 transmembrane transport protein seems to be the prior channel of the organic nanotube in the delivery process to vegetable cells. The etiolated wheat coleoptile bioassay demonstrated that the encapsulated herbicides have improved the bioactivity of free compounds, keeping 60% of inhibition of the weed at least for every disulfide, a requisite for their fruitful application as agrochemicals.

Peroxisome-targeted Supramolecular Nanoprobes Assembled with Pyrene-labelled Peptide Amphiphiles

Despite the versatile metabolic functions of peroxisomes such as lipid synthesis and fatty acid oxidation and their relevance to genetically inherited diseases, namely, peroxisome biogenesis disorders and peroxisomal enzyme deficiency, there is not much research on peroxisome-targeting therapeutics. Herein we present supramolecular nanostructured probes based on the self-assembly of peptide amphiphiles (PAs) having peroxisome-targeting ability in mammalian cells. The PA was designed to include the peroxisome-targeting tripeptide (SKL) and a fluorescent dye (pyrene). It was revealed that the presence of the SKL-appended carboxyl terminal group of PA, the extent of α-helical nature of the peptide block, and the fibrillar morphology of nano-assemblies affected the targeting efficiency of PA supramolecular nanoprobe. The simple modification of PAs by the peroxisome-targeting strength prediction showed an enhanced peroxisome specificity, as expected. This work provides important insights into designing subcellular organelle-targeting nanoparticles for next-generation nanomedicines.

Engineering the Kinetics of Directed Self-Assembly of Block Copolymers toward Fast and Defect-Free Assembly

Directed self-assembly (DSA) of block copolymers (BCPs) can achieve perfectly aligned structures at thermodynamic equilibrium, but the self-assembling morphology can become kinetically trapped in defective states. Understanding and optimizing the kinetic pathway toward domain alignment is crucial for enhancing process throughput and lowering defectivity to levels required for semiconductor manufacturing, but there is a dearth of experimental, three-dimensional studies of the kinetic pathways in DSA. Here, we combined arrested annealing and TEM tomography to probe the kinetics and structural evolution in the chemoepitaxy DSA of PS- b-PMMA with density multiplication. During the initial stages of annealing, BCP domains developed independently at first, with aligned structures at the template interface and randomly oriented domains at the top surface. As the grains coarsened, the assembly became cooperative throughout the film thickness, and a metastable stitch morphology was formed, representing a kinetic barrier. The stitch morphology had a three-dimensional structure consisting of both perpendicular and parallel lamellae. On the basis of the mechanistic information, we studied the effect of key design parameters on the kinetics and evolution of structures in DSA. Three types of structural evolutions were observed at different film thicknesses: (1) immediate alignment and fast assembly when thickness < L₀ ( L₀ = BCP natural periodicity); (2) formation of stitch morphology for 1.25-1.45 L₀; (3) fingerprint formation when thickness >1.64 L₀. We found that the DSA kinetics can be significantly improved by avoiding the formation of the metastable stitch morphology. Increasing template topography also enhanced the kinetics by increasing the PMMA guiding surface area. A combination of 0.75 L₀ BCP thickness and 0.50 L₀ template topography achieved perfect alignment over 100 times faster than the baseline process. This research demonstrates that an improved understanding of the evolution of structures during DSA can significantly improve the DSA process.

Template-Free Synthesis of Highly Porous Boron Nitride: Insights into Pore Network Design and Impact on Gas Sorption

Production of biocompatible and stable porous materials, e.g., boron nitride, exhibiting tunable and enhanced porosity is a prerequisite if they are to be employed to address challenges such as drug delivery, molecular separations, or catalysis. However, there is currently very limited understanding of the formation mechanisms of porous boron nitride and the parameters controlling its porosity, which ultimately prevents exploiting the material's full potential. Herein, we produce boron nitride with high and tunable surface area and micro/mesoporosity via a facile template-free method using multiple readily available N-containing precursors with different thermal decomposition patterns. The gases are gradually released, creating hierarchical pores, high surface areas (>1900 m²/g), and micropore volumes. We use 3D tomography techniques to reconstruct the pore structure, allowing direct visualization of the mesopore network. Additional imaging and analytical tools are employed to characterize the materials from the micro- down to the nanoscale. The CO₂ uptake of the materials rivals or surpasses those of commercial benchmarks or other boron nitride materials reported to date (up to 4 times higher), even after pelletizing. Overall, the approach provides a scalable route to porous boron nitride production as well as fundamental insights into the material's formation, which can be used to design a variety of boron nitride structures.

A parameter for the assessment of the segmentation of TEM tomography reconstructed volumes based on mutual information

A method is proposed and verified for selecting the optimum segmentation of a TEM reconstruction among the results of several segmentation algorithms. The selection criterion is the accuracy of the segmentation. To do this selection, a parameter for the comparison of the accuracies of the different segmentations has been defined. It consists of the mutual information value between the acquired TEM images of the sample and the Radon projections of the segmented volumes. In this work, it has been proved that this new mutual information parameter and the Jaccard coefficient between the segmented volume and the ideal one are correlated. In addition, the results of the new parameter are compared to the results obtained from another validated method to select the optimum segmentation.

Quantitative Three-Dimensional Characterization of Block Copolymer Directed Self-Assembly on Combined Chemical and Topographical Prepatterned Templates

Characterization of the three-dimensional (3D) structure in directed self-assembly (DSA) of block copolymers is crucial for understanding the complex relationships between the guiding template and the resulting polymer structure so DSA could be successfully implemented for advanced lithography applications. Here, we combined scanning transmission electron microscopy (STEM) tomography and coarse-grain simulations to probe the 3D structure of P2VP-b-PS-b-P2VP assembled on prepatterned templates using solvent vapor annealing. The templates consisted of nonpreferential background and raised guiding stripes that had PS-preferential top surfaces and P2VP-preferential sidewalls. The full 3D characterization allowed us to quantify the shape of the polymer domains and the interface between domains as a function of depth in the film and template geometry and offered important insights that were not accessible with 2D metrology. Sidewall guiding was advantageous in promoting the alignment and lowering the roughness of the P2VP domains over the sidewalls, but incommensurate confinement from the increased topography could cause roughness and intermittent dislocations in domains over the background region at the bottom of the film. The 3D characterization of bridge structures between domains over the background and breaks within domains on guiding lines sheds light on possible origins of common DSA defects. The positional fluctuations of the PS/P2VP interface between domains showed a depth-dependent behavior, with high levels of fluctuations near both the free surface of the film and the substrate and lower fluctuation levels in the middle of the film. This research demonstrates how 3D characterization offers a better understanding of DSA processes, leading to better design and fabrication of directing templates.