Original Micrographs Research Articles

Ревизия таксономического статуса Mallomonas multiunca var. pocosinensis на основании ультраструктуры кремнеземных покровов клетки, Mallomonas pocosinensis comb. et stat. nov.

The ultrastructure of the silica scales and bristles of two morphologically similar taxa, Mallomonas multiunca var. multiunca and M. multiunca var. pocosinensis, was compared. Based on the revealed differences in the morphology of scales and bristles, the taxonomic status of the species M. multiunca var. pocosinensis was revised and a new taxonomic combination, Mallomonas pocosinensis comb. stat. nov., was proposed. Аn updated description and original SEM micrographs are provided.

Taxonomy and Distribution of the Genus Sellaphora Mereschowsky (Bacillariophyceae: Sellaphoraceae) in Aquatic Ecosystems of Mongolia.

During our investigation, 28 species belonging to the genus Sellaphora Mereschowsky were found in different types of water bodies and streams in Mongolia. Of these, 14 species have already been described and/or shown earlier in the flora of Mongolia, and we found 14 species for the first time. One new taxonomic combination has been proposed: Sellaphora glomus (J.R. Carter and A.E. Bailey-Watts) Glushchenko and Kulikovskiy comb. nov. One species is proposed for description as new to science: Sellaphora dorofeyukae Glushchenko and Kulikovskiy sp. nov. All species were illustrated with original light micrographs, and a number of species were also illustrated with scanning electronic photographs. The distribution of the identified species within Mongolia and the world is discussed.

Down Syndrome detection with Swin Transformer architecture

Objective:Down Syndrome, also known as Trisomy 21, is a severe genetic disease caused by an extra chromosome 21. For the detection of Trisomy 21, despite those statistical methods have been widely used for screening, karyotyping remains the gold standard and the first level of testing for diagnosis. Due to karyotyping being a time-consuming and labour-intensive procedure, Computer Vision methodologies have been explored to automate the karyotyping process for decades. However, few studies have focused on Down Syndrome detection with the Transformer technique. This study develops a Down-Syndrome-Detector (DSD) architecture based on the Transformer structure, which includes a segmentation module, an alignment module, a classification module, and a Down Syndrome indicator. Methods:The segmentation and classification modules are designed by homogeneous transfer learning at the model level. Transfer learning techniques enable a network to share weights learned from the source domain (e.g., millions of data in ImageNet) and optimize the weights with limited labeled data in the target domain (e.g., less than 6,000 images in BioImLab). The Align-Module is designed to process the segmentation output to fit the classification dataset, and the Down Syndrome Indicator identifies a Down Syndrome case from the classification output. Results:Experiments are first performed on two public datasets BioImLab (119 cases) and Advanced Digital Imaging Research (ADIR, 180 cases). Our performance metrics indicate the good ability of segmentation and classification modules of DSD. Then, the DS detection performance of DSD is evaluated on a private dataset consisting of 1084 cells (including 20 DS cells from 2 singleton cases): 90.0% and 86.1% for cell-level TPR and TNR; 100% and 96.08% for case-level TPR and TNR, respectively. Conclusion:This study develops a pipeline based on the modern Transformer architecture for the detection of Down Syndrome from original metaphase micrographs. Both segmentation and classification models developed in this study are assessed using public datasets with commonly used metrics, and both achieved good results. The DSDproposed in this study reported satisfactory singleton case-specific DS detection results. Significance: As verified by a medical specialist, the developed method may improve Down Syndrome detection efficiency by saving human labor and improving clinical practice.

The progressive spectral signal-to-noise ratio of cryo-electron micrograph movies as a tool to assess quality and radiation damage

Background and ObjectiveThe quality of a cryoEM reconstruction is fundamentally a function of the signal-to-noise ratio (SNR) of the original micrographs. The SNR embodies multiple aspects of image formation, including microscope details and alignment, specimen composition and thickness, how it is recorded, and how the specimen degrades during imaging. With the advent of direct electron detectors and the recording of a series of images for each micrograph (a movie), we have an opportunity to count every electron and derive fully quantitative results. After alignment of the movie frames of a micrograph, we can calculate the SNR, or its spatial frequency equivalent, the spectral SNR (SSNR). This SSNR reflects residual movement between frames and the progressive effect of radiation damage. The goal is to develop a quantitative analysis of the SSNR and radiation damage to assess and improve the quality of micrographs. MethodsSeveral test cases were selected from the EMPIAR database and ten micrograph movies downloaded for each case. The movie frames were aligned as rigid bodies to compensate for stage and support movement. The SSNR for subsets of frames was then calculated to assess the effect of residual movement. The progressive SSNR (PSSNR) was subsequently calculated to determine the decrease in signal accumulation as a result of radiation damage. ResultsIn all cases the alignment of the movie frames compensated for global movement to the extent that the effect on the SSNR is negligible. The subset SSNR can be used as a tool to further confirm the extent of residual movement. The progressive SSNR indicates an increase in value up to an asymptote, consistent with the theory for radiation damage. Fitting these curves gives the inherent SNR before exposure, and the critical dose, which decreases with spatial frequency with an exponential parameter roughly between one and two. ConclusionsThe implementation of the PSSNR for movie frames provides a tool for assessing micrograph quality and progression of radiation damage. The estimation of the critical dose further quantifies radiation damage and may shed some light on the mechanisms of damage. These are likely both a function of the specimen composition and the imaging parameters used.

Image-based semi-multiscale finite element analysis using elastic subdomain homogenization

In this paper we present a semi-multiscale methodology, where a micrograph is split into multiple independent numerical model subdomains. The purpose of this approach is to enable a controlled reduction in model fidelity at the microscale, while providing more detailed material data for component level- or more advanced finite element models. The effective anisotropic elastic properties of each subdomain are computed using periodic boundary conditions, and are subsequently mapped back to a reduced mesh of the original micrograph. Alternatively, effective isotropic properties are generated using a semi-analytical method, based on averaged Hashin–Shtrikman bounds with fractions determined via pixel summation. The chosen discretization strategy (pixelwise or partially smoothed) is shown to introduce an uncertainty in effective properties lower than 2% for the edge-case of a finite plate containing a circular hole. The methodology is applied to a aluminium alloy micrograph. It is shown that the number of elements in the aluminium model can be reduced by 99.89% while not deviating from the reference model effective material properties by more than 0.65%, while also retaining some of the characteristics of the stress-field. The computational time of the semi-analytical method is shown to be several orders of magnitude lower than the numerical one.

Chromosome Extraction Based on U-Net and YOLOv3

Karyotype analysis based on chromosome banding and microscopic imaging is an important means for the diagnosis of genetic symptoms. Chromosome extraction is one of the key steps in karyotype analysis, but it faces some complex situations i.e. chromosome overlaps and adhesions, which are still a challenge for traditional algorithms. Here, we proposed a method for chromosome extraction based on deep learning. In this method, U-Net was used to segment the original micrographs to remove background noise such as nuclei and other interferences. Then YOLOv3 was used to detect and extract each chromosome. Further, U-Net was used again to extract the single chromosomes precisely. The results show that this method can remove effectively the interferences outside the chromosomes, and accurately extract the overlapping and adhesive chromosomes. The accuracy of extracting chromosomes from the raw G-band chromosome images reaches 99.3%. This method is of great significance for the development of automatic karyotype analysis technology.

Cover Image, Volume 102, Issue 8

Cover Photograph: Image segmentation process for grain size analysis, with a) original SE micrograph, b) micrograph with traced grain boundaries, c) black and white threshold image and d) final grain count produced by ImageJ. Image Credit: Ms. Jamesa Stokes (The Pennsylvania State University). DOI: 10.1111/jace.16317. image

PIXER: an automated particle-selection method based on segmentation using a deep neural network

BackgroundCryo-electron microscopy (cryo-EM) has become a widely used tool for determining the structures of proteins and macromolecular complexes. To acquire the input for single-particle cryo-EM reconstruction, researchers must select hundreds of thousands of particles from micrographs. As the signal-to-noise ratio (SNR) of micrographs is extremely low, the performance of automated particle-selection methods is still unable to meet research requirements. To free researchers from this laborious work and to acquire a large number of high-quality particles, we propose an automated particle-selection method (PIXER) based on the idea of segmentation using a deep neural network.ResultsFirst, to accommodate low-SNR conditions, we convert micrographs into probability density maps using a segmentation network. These probability density maps indicate the likelihood that each pixel of a micrograph is part of a particle instead of just background noise. Particles selected from density maps have a more robust signal than do those directly selected from the original noisy micrographs. Second, at present, there is no segmentation-training dataset for cryo-EM. To enable our plan, we present an automated method to generate a training dataset for segmentation using real-world data. Third, we propose a grid-based, local-maximum method to locate the particles from the probability density maps. We tested our method on simulated and real-world experimental datasets and compared PIXER with the mainstream methods RELION, DeepEM and DeepPicker to demonstrate its performance. The results indicate that, as a fully automated method, PIXER can acquire results as good as the semi-automated methods RELION and DeepEM.ConclusionTo our knowledge, our work is the first to address the particle-selection problem using the segmentation network concept. As a fully automated particle-selection method, PIXER can free researchers from laborious particle-selection work. Based on the results of experiments, PIXER can acquire accurate results under low-SNR conditions within minutes.

Petalomonas sphagnophila (Euglenophyta, Petalomonadales), a new euglenophyte species for Russia

Petalomonas sphagnophila has been found for the first time in Russia from the Shichengskoe raised bog (Vologda Region). Morphology of the species is studied by means of light microscopy and illustrated by original micrographs. The data on its taxonomy, ecology and distribution are given. The name P. sphagnophila was not validly published because no type was indicated in the original publication (Christen, 1962), so we are validating the name by indicating its holotype. P. polytaphrena Skuja, nom. inval. is treated as a synonym of P. sphagnophila. Currently, thirty species of the genus Petalomonas, including P. sphagnophila, are known from Russia.

Issue Cover (May 2015)

Front cover: Immature oligodendrocytes show complex morphology as revealed by Rip immunostaining. Oligodendrocyte progenitor cells were prepared from P1 rat forebrain and were differentiated into immature oligodendrocytes under defined medium condition. Cells were immunostained with anti-oligodendrocyte (Rip) antibody (green), nuclei were counter-stained with propidium iodide (red) (original micrograph G of the lower panel in Figure 3). Images were acquired by a QICLICK monochrome digital camera attached to an Olympus BX60 fluorescence microscope with 40x objective lens. J. Neurochem. 2015, vol. 133 (4), pp. 532–543. Read the full article on doi: 10.1111/jnc.12988

A new morphotype of chrysophycean stomatocyst from the pond of Peter the Great Botanical Garden (Saint Petersburg)

The paper deals with the problem of identifying chrysophycean stomatocysts. An historical essay of classification schemes for chrysophycean stomatocysts is presented. It is noted that the stomatocysts are widely used in palaeolimnological studies. A new 395/13 morphotype of a chrysophycean stomatocyst from the pond of Peter the Great Botanical Garden is described on the basis of plankton samples. The stomatocyst is spherical (5.3 μm diam.) and has a short cylindrical collar (1.8 μm diam., 0.2 μm high), with a conical pore (0.3 μm diam.). The entire stomatocyst surface is covered with rounded scabrae 0.1–0.2 μm in diameter. Morphology of the new stomatocyst morphotype was studied and its original micrograph was made with a scanning electron microscope.

Phytoplankton diversity during the spring bloom in the northwestern Mediterranean Sea

The section of the Liguro-Provençal basin north of the Balearic Islands is one of the most productive sites in the whole Mediterranean Sea, with intense phytoplankton bloom lasting about 2 months in late winter-early spring. The phytoplankton species composition of the area was investigated using light and electron microscopy to analyze bottle and net samples collected at several stations in spring 2000 and 2003. Serial dilution cultures established from bottle samples were also examined. A total of 168 phytoplankton taxa was identified, consisting of 73 Coscinodiscophyceae, 47 Dinophyceae, 25 Coccolithophyceae and 4 Prymnesiophyceae, 5 Prasinophyceae, 3 Chrysophyceae, 2 Cryptophyceae, 2 Dictyochophyceae, 1 Euglenophyceae, 1 Pelagophyceae, 1 Choanoflagellidea, 1 Filosea and 3 incertae sedis . We also provided a brief taxonomic description and original micrographs for 25 of the smallest and/or less known species identified in the study area, which may go undetected during routine microscopical analysis of fixed samples. Among these, 10 species were recorded for the first time in the Mediterranean Sea, confirming the need of detailed studies to reveal the biodiversity and biogeography of Mediterranean phytoplankton.

Depressorotunda gen. nov., a new remarkable Uropodina mite genus from South-East Asia with description of four new species (Acari: Mesostigmata)

A new genus Depressorotunda gen. nov. and four new species are described from South-East Asia, namely Depressorotunda malayana sp. nov. and Depressorotunda seticaudata sp. nov. from Malaysia, Depressorotunda thailandica sp. nov. from Thailand and Depressorotunda mirifica sp. nov. from Vietnam. A key to the species of the genus Depressorotunda is provided with 28 original drawings and scanning micrographs.

Notes on Kaszabjbaloghia with the description of a new species from Ecuador (Acari: Mesostigmata: Uropodidae)

Kaszabjbaloghia Hirschmann, 1973, distributed in South-America, is characterized by the following combination of characters: reduced marginal shield, posteromarginal setae placed on membranous cuticle on the dorsal idiosoma, linguliform genital shield in females, oval or egg-like genital shield bearing one pair needle-like setae in males, and the characteristic shape of peritremes. In this contribution, I provide short redescriptions of the known species of Kaszabjbaloghia and describe a new species, K. ecuadorica sp. nov., from Ecuador. The new species is similar to K. kaszabi Hirschmann, 1973, but differs from the latter in the ornamentation of genital shield of the female and the number of sternal cavities. Additionally, we transfer K. hirschmanni Hiramatsu, 1978 to Hutufeideria Hirschmann & Hirmatsu, 1977 (as Hutufeideria hirschmanni (Hiramatsu, 1978) comb. nov.) on the basis of the following: setation of dorsal shield, ornamentation of caudal part of the dorsal shield, shape of hypostomal setae, shape of internal malae and setation of the palp. An identification key to the species of Kaszabjbaloghia is also provided. Original illustrations and scanning micrographs are provided for all species.

New Uropodina species (Acari: Mesostigmata) and records from Kenya

Chelonuropoda africana sp. n. is described with original drawings and scanning micrographs. New records of two other Uropodina species, Neodiscopoma crenulatum Marais et Theron, 1986 and Rotundabaloghia feherdii Kontschan, 2004 from Kenya are given.

The puparium and mature larva of the flat-footed fly Lindneromyia hungarica Chandler, 2001 (Diptera: Platypezidae)

The puparium/mature larva of Lindneromyia hungarica Chandler, 2001 is described in detail for the first time and documented by original drawings and SEM micrographs. The puparium is formed from the cuticle of the mature larva and thus bears all larval cuticular structures. Cuticular structures and diagnostic characters of L. hungarica are clearly different from L. dorsalis Meigen, 1804, till this time the only European species of the genus Lindneromyia for which the puparium had been described. A new identification key to the puparia/mature larvae of both species is provided.

NEW TAXONS OF BENTHIC DIATOM ALGAE OF THE TILIGUL ESTUARY (THE NORTH-WESTERN PART OF THE BLACK SEA COAST)

181 species and taxons of the diatom algae were revealed in benthos of the Tiligul Estuary. 74 of them are represented for the reservoir for the first time and 25 for the first time for the estuaries of the north-western part of the Black Sea. Cocconeis scutellum var. tiligulicus Kovtun var. nov. and Fallacia gusliakovi Kovtun sp. nov. are described as new species for science. The original micrographs are presented.

Description of Metagynella masani sp. n. from Kenya (Acari: Uropodina)

The third African Metagynella Berlese, 1919 species (Metagynella masani sp. n.) is described in this paper. Original drawing and scanning micrographs of the new species are given.

Comparison of fractal and profilometric methods for surface topography characterization

In this study microstructural and roughness characterization of surface of aluminium foils used in lithographic printing process was performed by contact and non-contact profilometric methods and fractal analysis. Significant differences in roughness parameters values inferred from stylus method in respect to those inferred from the non-contact measurements were observed. The investigation of correlation between various fractal dimensions obtained from gray-scale SEM micrographs and binary images resulting from median filtering of the original SEM micrographs as well as selected relevant roughness parameters shows that there is a strong correlation between certain roughness parameters and particular fractal dimensions. This correlations permit better physical understanding of fractal characteristics and interpretation of the dynamics of surface roughness change through processing. Generally these correlations are more suitable for parameters obtained by stylus method than those inferred from the laser-based measurements.

Strombomonas and Trachelomonas species (Euglenophyta) from south-eastern USA

A biogeographical and taxonomic study on Strombomonas and Trachelomonas, which are often abundant in polluted environments, was undertaken in south-eastern USA. Light and scanning electron microscope analysis allowed the identification of 68 taxa, among them five Strombomonas and 63 Trachelomonas. All are documented with original SEM and LM micrographs. Twenty-seven Trachelomonas taxa are reported as new from this region. Variability in lorica microstructure is demonstrated for T. curta var. curta, T. pusilla var. punctata, T. rotunda, T. hispida var. coronata and T. scabra var. scabra from natural habitats. Physicochemical parameters for water quality at the collection sites are reported.