Reducing manual operation time to obtain a segmentation learning model for volume electron microscopy using stepwise deep learning with manual correction.

Three-dimensional (3D) observation of a biological sample using serial-section electron microscopy is widely used. However, organelle segmentation requires a significant amount of manual time. Therefore, several studies have been conducted to improve organelle segmentation's efficiency.

Degradation of insulin amyloid by antibiotic minocycline and formation of toxic intermediates.

Insulin balls, localized insulin amyloids formed at subcutaneous insulin-injection sites in patients with diabetes, cause poor glycemic control owing to impairments in insulin absorption. Our previous study has shown that some insulin balls are cytotoxic, but others are not, implying amyloid polymorphism. Interestingly, the patient with toxic insulin balls had been treated with antibiotic minocycline, suggesting a possible relationship between toxicity of insulin balls and minocycline.

Local surface plasmon resonance of gold nanoparticles as a correlative light and electron microscopy (CLEM) tag for biological samples.

In this study, we investigated use of local surface plasmon resonance (LSPR) of metal nanoparticles (NPs) as a correlative light and electron microscopy (CLEM) tag for biological samples. Gold NPs in ultra-thin sections for TEM revealed that LSPR could be observed by optical microscopy at sizes of 20 nm or larger. Gold NPs at sizes less than 20 nm could be observed using the gold enhancement method.

Practical method of cell segmentation in electron microscope image stack using deep convolutional neural network☆.

Segmentation of three-dimensional (3D) electron microscopy (EM) image stacks is an arduous and tedious task. Deep convolutional neural networks (CNNs) work well to automate the segmentation; however, they require a large training dataset, which is a major impediment. In order to solve this issue, especially for sparse segmentation, we used a CNN with a minimal training dataset.

Development of novel correlative light and electron microscopy linkage system using silicon nitride film.

In this study, we investigated the optical properties of a silicon nitride (SiN) film. The thin SiN film (30 nm thick) exhibited good light transmittance and little autofluorescence and could be used as a microscope slide for optical microscopy (OM). In addition, we developed a novel correlative light and electron microscopy (CLEM) that combines OM with transmission electron microscopy (TEM) using an SiN thin film.

Evaluation of lanthanide salts as alternative stains to uranyl acetate.

Uranyl acetate (UAc) has been generally used not only as a superb staining reagent for ultrathin sections of plastic-embedded biological materials, but also as high-contrast negative stains for biological macromolecules such as particles of protein or virus. However, the use and purchase of radioactive UAc have been restricted. In this study, we determine the performance of ytterbium triacetate, lutetium triacetate, samarium triacetate and gadolinium triacetate as new staining reagents for biological electron microscopy.

New versatile staining reagents for biological transmission electron microscopy that substitute for uranyl acetate.

Aqueous uranyl acetate has been extensively used as a superb staining reagent for transmission electron microscopy of biological materials. However, recent regulation of nuclear fuel material severely restricts its use even for purely scientific purposes. Since uranyl salts are hazardous due to biological toxicity and remaining radioactivity, development of safe and non-radioactive substitutes is greatly anticipated.

The advanced ion-milling method for preparation of thin film using ion slicer: application to a sample recovered from diamond-anvil cell.

The advanced argon ion-milling technique using a new instrument called ion slicer was newly developed for preparation of thin foil. Compared to the conventional ion-milling methods, this technique facilitates very wide area to be homogeneously thinned by rocking the ion beam source with low angle and the specimen during milling. Here we applied this technique to a sample recovered from a laser-heated diamond-anvil cell (DAC).

Observation of the three-dimensional structure of actin bundles formed with polycations.

Three-dimensional structures of actin bundles formed with polycations were observed by using transmission electron microtomography and atomic force microscopy. We found, for the first time, that the cross-sectional morphology of actin bundles depends on the polycation species and ionic strength, while it is insensitive to the degree of polymerization and concentration of polycation. Actin bundles formed with poly-N-[3-(dimethylamino)propyl] acrylamide methyl chloride quaternary show a ribbon-like cross-sectional morphology in low salt concentrations that changes to cylindrical cross-sectional morphology with hexagonal packing of the actin filaments in high salt concentrations.

Spatial arrangement of metal nanoparticles supported by porous polymer substrates studied by transmission electron microtomography.

Fine metal particles (nanoparticles) stabilized on porous (polymeric) substrates can be considered as a model system of a high-performance catalyst. In the present study, the substrate was made using the periodic microphase-separated structure of a block copolymer as the template, and the Pd nanoparticles were formed inside the porous material by reduction of the Pd2+ ions with 1-propanol as the reductant. The three-dimensional morphology of such a polymer-Pd hybrid material was studied by transmission electron microtomography.

Transmission electron microtomography without the "missing wedge" for quantitative structural analysis.

A three-dimensional (3D) visualization and structural analysis of a rod-shaped specimen of a zirconia/polymer nanocomposite material were carried out by transmission electron microtomography (TEMT) with particular emphasis on complete rotation of the specimen (tilt angular range: +/-90 degrees ). In order to achieve such an ideal experimental condition for the TEMT, improvements in the specimen as well as the sample holder were made. A rod-shaped specimen was necessary in order to obtain a high transmission of the specimen upon tilting to large angles.

Reduction of anisotropic image resolution in transmission electron microtomography by use of quadrangular prism-shaped section.

A quadrangular prism specimen (a 'prism-shaped' section) was observed in three-dimension (3-D) by transmission electron microtomography (TEMT) over as wide a tilt range as possible. Two types of specimens were prepared for the TEMT experiments: (i) a prism-shaped section of a block copolymer nanostructure, whose cross section was 200 nm on each side and (ii) a conventional ultrathin section having the same thickness (approximately 200 nm) as the prism-shaped section. Image quality of the projections taken at high tilt angles, e.

The spindle pole body of the pathogenic yeast Exophiala dermatitidis: variation in morphology and positional relationship to the nucleolus and the bud in interphase cells.

The spindle pole body (SPB) in the interphase cell of the pathogenic yeast Exophiala dermatitidis was studied in detail. The SPB was located on the outer nuclear envelope and was 342 +/- 86 nm long in a haploid strain. It consisted of two disk elements that measured 151 +/- 43 nm in diameter and 103 +/- 17 nm in thickness, connected by a rod-shaped midpiece that measured 56 +/- 20 nm in length and 37 +/- 9 nm in diameter.