scholarly journals Virtual Systematics with Annotate: The Mexican archaeocyaths example

2020 ◽  
Vol 4 ◽  
Author(s):  
Lucile-Morgane Hays ◽  
Adeline Kerner
Keyword(s):  
Thin Section ◽  
Image Annotation ◽  
Single Species ◽  
Working Time ◽  
Online Publishing ◽  
Descriptive Data ◽  
Online Data ◽  
Thin Sections ◽  
Points Of Interest ◽  
Collection Number

Digitization and online publishing of museum specimen data are happening worldwide. Studies based solely on online data become increasingly accessible. The current events, for example, reducing our transport-related carbon footprint or the COVID-19 pandemic, provide key opportunities to highlight the full value of digitized collections and their related tools, which allow us to continue our research from home or at least without travelling. Are existing data resources and tools adequate for engaging in a research project from beginning to end? To address this issue, we propose to use the Mexican archaeocyaths digitized collection from the Museum National d’Histoire Naturelle, Paris, France (MNHN) and the freeware Annotate in order to describe and identify all the archaeocyaths from the Mexican Cambrian reef. Archaeocyaths are aspiculate sponges that lived during the Cambrian Period. They were the first animals to build reefs. In the MNHN collection, they are found as thin-sections with several archaeocyaths per thin-section (Fig. 1). Multiple individuals are grouped under a single collection number and a single species name. The list of species in the thin-section is only captured on the paper label, and cannot currently be found online. To study an archaeocyaths' reef, the archaeocyaths have to be described and identified one by one, and the location of each specimen has to be accuratly captured. Is it possible to do this with Annotate? Can a palaeontologist use only digitized specimens and Annotate to study a complete fauna of a given time and space? Annotate is an image annotation tool for the natural sciences. It allows users to measure, count, and tag all the morphological structures of an organism. Photos may be imported from the Recolnat database or users may import their own photos. Users can measure lengths, surfaces, and angles, count occurrences and add points of interest. Users can also tag the different individuals to identify them. Morphological terms may be imported as a standardized list from Xper2 or Xper3. Xper3 is a web platform that manages descriptive data and provides interactive identification keys. The results of the measurements and annotations can be exported into CSV format (comma-separated values) or into a structured descriptive data (SDD) format. To identify an archaeocyath to genus level, we need to identify morphological structures and count the occurrence of some of them, and for an identification to the species level, we need to measure different additional parts. The standardized list of morphological terms has been imported from the archaeocyaths genera knowledge base and the list of measurements has been created directly in Annotate. Lengths (e.g., pore size, cup diameter), counts (e.g., number of septae, number of pores) and points of interest (e.g., tumuli, canals, septa) are easy to use. What are the key lessons learnt to remember at the end of this study? The digitized archaeocyaths from Mexico have been identified as easily with Annotate as if a microscope and thin sections were used. The CSV export provided quick access to statistics calculations. The main difference between a microscope and Annotate is the working time. Some functionalities of Annotate are not optimized, their uses are time consuming. For instance, the importation of photos is not really appropriate for archaeocyaths studies. Two sections (transversal and longitudinal) per specimen are necessary to see all the morphological structures. These two parts of the same rock are packed together with one collection number. While users can easily switch from one section to another with a microscope, they can not with Annotate. Annotate allows only one photo per collection number from Recolnat, but not images of the two sections and their metadata. The main difference between a microscope and Annotate is the working time. Some functionalities of Annotate are not optimized, their uses are time consuming. For instance, the importation of photos is not really appropriate for archaeocyaths studies. Two sections (transversal and longitudinal) per specimen are necessary to see all the morphological structures. These two parts of the same rock are packed together with one collection number. While users can easily switch from one section to another with a microscope, they can not with Annotate. Annotate allows only one photo per collection number from Recolnat, but not images of the two sections and their metadata. Although Annotate is not an intuitive tool to use it is still very powerful however, some training is required to fully take advantage of it, and there is no documentation available. This freeware has great potential as it can assist researchers in their work and proposes an alternative to the need to travel around the world to study a fossil.

scholarly journals Superpixel segmentations for thin sections: evaluation of methods to enable the generation of machine learning training data sets

2021 ◽  
Author(s):  
Jiaxin Yu ◽  
Florian Wellmann ◽  
Simon Virgo ◽  
Marven von Domarus ◽  
Mingze Jiang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Thin Section ◽  
Image Annotation ◽  
Performance Testing ◽  
Training Image ◽  
Training Data ◽  
Sandstone Sample ◽  
Thin Sections ◽  
Superpixel Segmentation

Training data is the backbone of developing either Machine Learning (ML) models or specific deep learning algorithms. The paucity of well-labeled training image data has significantly impeded the applications of ML-based approaches, especially the development of novel Deep Learning (DL) methods like Convolutional Neural Networks (CNNs) in mineral thin section images identification. However, image annotation, especially pixel-wise annotation is always a costly process. Manually creating dense semantic labels for rock thin section images has been long considered as an unprecedented challenge in view of the ubiquitous variety and complexity of minerals in thin sections. To speed up the annotation, we propose a human-computer collaborative pipeline in which superpixel segmentation is used as a boundary extractor to avoid hand delineation of instances boundaries. The pipeline consists of two steps: superpixel segmentation using MultiSLIC, and superpixel labeling through a specific-designed tool. We use a cutting-edge methodology Virtual Petroscopy (ViP) for automatic image acquisition. Bentheimer sandstone sample is used to conduct performance testing of the pipeline. Three standard error metrics are used to evaluate the performance of MultiSLIC. The result indicates that MultiSLIC is able to extract compact superpixels with satisfying boundary adherence given multiple input images. According to our test results, large and complex thin section images with pixel-wisely accurate labels can be annotated with the labeling tool more efficiently than in a conventional, purely manual work, and generate data of high quality.

scholarly journals Review of Post-embedding Immunogold Methods for the Study of Neuronal Structures

2021 ◽  
Vol 15 ◽  
Author(s):  
Ronald S. Petralia ◽  
Ya-Xian Wang
Keyword(s):  
Thin Section ◽  
Gold Particle ◽  
Freeze Substitution ◽  
Particle Sizes ◽  
Neuronal Function ◽  
Double Labeling ◽  
Thin Sections ◽  
Transmission Electron ◽  
Functional Localization ◽  
Neuronal Tissues

The post-embedding immunogold (PI) technique for immunolabeling of neuronal tissues utilizing standard thin-section transmission electron microscopy (TEM) continues to be a prime method for understanding the functional localization of key proteins in neuronal function. Its main advantages over other immunolabeling methods for thin-section TEM are (1) fairly accurate and quantifiable localization of proteins in cells; (2) double-labeling of sections using two gold particle sizes; and (3) the ability to perform multiple labeling for different proteins by using adjacent sections. Here we first review in detail a common method for PI of neuronal tissues. This method has two major parts. First, we describe the freeze-substitution embedding method: cryoprotected tissue is frozen in liquid propane via plunge-freezing, and is placed in a freeze-substitution instrument in which the tissue is embedded in Lowicryl at low temperatures. We highlight important aspects of freeze-substitution embedding. Then we outline how thin sections of embedded tissue on grids are labeled with a primary antibody and a secondary gold particle-conjugated antibody, and the particular problems encountered in TEM of PI-labeled sections. In the Discussion, we compare our method both to earlier PI methods and to more recent PI methods used by other laboratories. We also compare TEM immunolabeling using PI vs. various pre-embedding immunolabeling methods, especially relating to neuronal tissue.

scholarly journals Preparation of Thin Sections

1998 ◽  
Vol 6 (7) ◽  
pp. 8-9
Author(s):  
Ian Chaplin
Keyword(s):  
Chemical Composition ◽  
Thin Section ◽  
Microprobe Analysis ◽  
Rock Sample ◽  
Rock Type ◽  
X Rays ◽  
Thin Sections ◽  
Economical Method ◽  
Optical Examination ◽  
Composition Of Minerals

The optical examination of a rock sample in thin section is the quickest and most economical method for classifying rock type and determining which analytical route to follow.Thin sections for transmitted light are the most common, but there are also:Polished Thin Sections • Polished sections are used for classification and identification of minerals that cannot be determined in standard thin sections. They are also essential for microprobe analysis. Minute mineral grains are analyzed by bombarding them with a focused bean of electrons, which generate x-rays, characteristic of the elements within the grains. X-rays are identified and quantified to determine the chemical composition of minerals.

Automation of Carbonate Rock Thin Section Description Using Cognitive Image Recognition

2021 ◽  
Author(s):  
Hesham Talaat Shebl ◽  
Mohamed Ali Al Tamimi ◽  
Douglas Alexander Boyd ◽  
Hani Abdulla Nehaid
Keyword(s):  
Thin Section ◽  
Image Recognition ◽  
Oil Recovery ◽  
Reservoir Rock ◽  
Supervised Machine Learning ◽  
Neural Net ◽  
Data Set ◽  
Thin Sections ◽  
Rock Quality ◽  
Pore Types

Abstract Simulation Engineers and Geomodelers rely on reservoir rock geological descriptions to help identify baffles, barriers and pathways to fluid flow critical to accurate reservoir performance predictions. Part of the reservoir modelling process involves Petrographers laboriously describing rock thin sections to interpret the depositional environment and diagenetic processes controlling rock quality, which along with pressure differences, controls fluid movement and influences ultimate oil recovery. Supervised Machine Learning and a rock fabric labelled data set was used to train a neural net to recognize Modified Durham classification reservoir rock thin section images and their individual components (fossils and pore types) plus predict rock quality. The image recognition program's accuracy was tested on an unseen thin section image database.

scholarly journals A thin-section and freeze-fracture study of microfilament-membrane attachments in choroid plexus and intestinal microvilli.

1978 ◽  
Vol 79 (3) ◽  
pp. 774-787 ◽  
Author(s):  
N S McNutt
Keyword(s):  
Choroid Plexus ◽  
Thin Section ◽  
Brush Border ◽  
Freeze Fracture ◽  
Similar Type ◽  
Heavy Meromyosin ◽  
Thin Sections ◽  
Intestinal Brush Border ◽  
Fracture Study ◽  
20 Nm

Choroid plexus and intestinal microvilli in thin sections have microfilaments in the cytoplasm adjacent to the membranes, and in replicas have broken strands of filaments in both cytoplasm and on E faces of plasm membranes. The microfilaments contain actin as indicated by their binding of heavy meromyosin (HMM). In sections of choroid plexus, the microfilaments are 7-8 nm in diameter and form a loose meshwork which lies parallel to the membrane and which is connected to the membranes both by short, connecting filaments (8 times 30 nm) and dense globules (approximately 15-20 nm). The filamentous strands seen in replicas are approximately 8 nm in diameter. Because they are similar in diameter and are connected to the membrane, these filamentous strands seen in replicas apparently represent the connecting structures, portions of the microfilaments, or both. The filamentous strands attached to the membrane are usually associated with the E face and appear to be pulled through the P half-membrane. In replicas of intestinal brush border microvilli, the connecting strands attaching core microfilaments to the membrane are readily visualized. In contrast, regions of attachment of core microfilaments to dense material at the tips of microvilli are associated with few particles on P faces and with few filamentous strands on the E faces of the membranes. Freeze-fracture replicas suggest a morphologically similar type of connecting strand attachment for microfilament-membrane binding in both choroid plexus and intestinal microvilli, despite the lack of a prominent core bundle of microfilaments in choroid plexus microvilli.

A novel methodological approach for thin-section description and its application to periglacially disturbed Pleistocene deposits from Danbury, Essex, UK

2011 ◽  
Vol 90 (4) ◽  
pp. 271-291 ◽  
Author(s):  
K. Leszczynska ◽  
J. Boreham ◽  
S. Boreham
Keyword(s):  
Thin Section ◽  
Systematic Approach ◽  
Methodological Approach ◽  
Main Process ◽  
Freezing And Thawing ◽  
Quaternary Deposits ◽  
Thin Sections ◽  
New Approach ◽  
C 50 ◽  
New Hypothesis

AbstractAlthough micromorphological terminology has been evolving since 1960, there have been few attempts to create a systematic approach to the description of thin-sections which would serve as a guiding tool for inexperienced researchers, students, and all new to the field of micromorphology. In this paper we present a novel, decision tree based systematic approach for thin-section description. This new approach attempts to unify micromorphological descriptions of Quaternary deposits, regardless of the character of the deposit and the purpose of the analysis.In this research project, named ‘Hidden Ice Worlds’, the micromorphology of an 8 m thick sequence of periglacially disturbed deposits from the Royal Oak Pit, Danbury hill, Essex, UK is described. This sequence is situated on the eastern side of Danbury hill, at c. 50 m OD. Based on micromorphological analyses, a new hypothesis for the evolution of this sequence is presented. Multiple phases of physical reworking associated with freezing and thawing of the deposit, subsequent to Elsterian (Anglian) glaciation (480-420 ka BP) is proposed as the main process responsible for the evolution of the sequence. As periglacially derived deposits are usually removed from such elevated locations on hill' slopes, inversion of the topography is proposed as a necessary factor for the formation and preservation of the sequence described in this atypical location.

scholarly journals Structure and Assembly of Intracellular Mature Vaccinia Virus: Thin-Section Analyses

2001 ◽  
Vol 75 (22) ◽  
pp. 11056-11070 ◽  
Author(s):  
Gareth Griffiths ◽  
Norbert Roos ◽  
Sybille Schleich ◽  
Jacomine Krijnse Locker
Keyword(s):  
Vaccinia Virus ◽  
Thin Section ◽  
Structural Organization ◽  
Integral Membrane Proteins ◽  
Thin Sections ◽  
Thin Section Electron Microscopy ◽  
Section Electron ◽  
Infected Cells ◽  
Preceding Study ◽  
Section Electron Microscopy

ABSTRACT In the preceding study (see accompanying paper), we showed by a variety of different techniques that intracellular mature vaccinia virus (vaccinia IMV) is unexpectedly complex in its structural organization and that this complexity also extends to the underlying viral core, which is highly folded. With that analysis as a foundation, we now present different thin-section electron microscopy approaches for analyzing the IMV and the processes by which it is assembled in infected HeLa cells. We focus on conventional epoxy resin thin sections as well as cryosections to describe key intermediates in the assembly process. We took advantage of streptolysin O's ability to selectively permeabilize the plasma membrane of infected cells to improve membrane contrast, and we used antibodies against bone fide integral membrane proteins of the virus to unequivocally identify membrane profiles in thin sections. All of the images presented here can be rationalized with respect to the model put forward for the assembly of the IMV in the accompanying paper.

scholarly journals Ice crystal c-axis orientation and mean grain size measurements from the Dome Summit South ice core, Law Dome, East Antarctica

2016 ◽  
Author(s):  
A. Treverrow ◽  
J. Li ◽  
T. H. Jacka
Keyword(s):  
Thin Section ◽  
Ice Core ◽  
Median Number ◽  
East Antarctica ◽  
Polar Coordinates ◽  
Depth Information ◽  
Data Set ◽  
Axis Orientation ◽  
Orientation Data ◽  
Thin Sections

Abstract. We present measurements of crystal c-axis orientations and mean grain area from the Dome Summit South (DSS) ice core drilled on Law Dome, East Antarctica. These data are from 185 individual thin sections obtained between a depth of 117 m below the surface and the bottom of the DSS core at a depth of 1196 m. The median number of c-axis orientations recorded in each thin section was 100, with values ranging from 5 through to 111 orientations. The data from all 185 thin sections are provided in a single comma separated value (csv) formatted file which contains the c-axis orientations in polar coordinates, depth information for each core section from which the data were obtained, the mean grain area calculated for each thin section and other data related to the drilling site. The data set is also available as a MATLAB™ structure array. Additionally, the c-axis orientation data from each thin of the 185 thin sections are summarised graphically in figures containing a Schmidt diagram, histogram of c-axis colatitudes and rose plot of c-axis azimuths. All of these data are referenced by doi:10.4225/15/5669050CC1B3B and are available free of charge at https://data.antarctica.gov.au.

Upscaling lithology and porosity-type fractions from the micro- to the core-scale with thin-section petrography, dual-energy computed tomography, and rock typing: Creation of diagenesis and porosity-type logs

2019 ◽  
Vol 7 (1) ◽  
pp. B9-B32 ◽  
Author(s):  
Jacob M. Proctor ◽  
André W. Droxler ◽  
Naum Derzhi ◽  
Heath H. Hopson ◽  
Paul (Mitch) Harris ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Thin Section ◽  
Dual Energy ◽  
Depositional Facies ◽  
Thin Sections ◽  
Average Percentage ◽  
The Core ◽  
Diagenetic Alteration ◽  
Rock Typing ◽  
Mason County

We have developed and validated a new approach to upscale lithology and porosity-type fractions from thin sections to cores using dual energy and multiscale computed tomography (CT). A new rock-typing approach (genetic rock typing [GRT]) is proposed to upscale ⇋diagenetic mineral and diagenetic pore-type fractions, from thin sections to the core domain, eventually to create a diagenesis and porosity types logs. An extensive set of short cores from Mason County (Texas) provides a representative sample set of Late Cambrian microbial buildups and their interbuildup sediments to test the GRT approach. GRTs were defined by using a dolomite log as a proxy for diagenesis and the average percentage of dolomite from each observed depositional facies (buildup interior, buildup rind, and interbuildup sediment) as a cutoff. Dolomite, diagenetic calcite, and diagenetic porosity fractions are summed to form a diagenesis log, which captures depositional facies and the diagenetic overprint at a 0.5 mm resolution. The diagenesis log was subdivided based on the number of pore-throat size classes within each GRT and provided a framework to distribute porosity-type fractions from thin sections to log form. A high correlation coefficient is observed when the predicted extent of diagenetic alteration from the log is compared with that quantified for each thin section using image processing ([Formula: see text]). Multiscale CT imaging and dual-energy-derived logs could be directly linked to well-log photoelectric factor and bulk-density logs. This approach thus has the ability to span six orders of magnitude in resolution (500–0.0005 mm). The diagenesis log can be used to extrapolate porosity-type fractions from thin sections to logs, from which qualitative geologic interpretations can be generally translated into quantitative values.

Contamination of thin sections, cause and elimination

1978 ◽  
Vol 36 (2) ◽  
pp. 78-79 ◽  
Author(s):  
Hilton H. Mollenhauer ◽  
D. James Morré
Keyword(s):  
Thin Section ◽  
Surface Contamination ◽  
Thin Sections ◽  
Section Surface ◽  
Extraneous Material ◽  
Possible Cause

Contamination of thin sections is a problem that has undoubtedly been experienced by most, if not all, electron microscopists. By section contamination, we refer to any extraneous material in, or on, a thin section. Section contamination is not only a nuisance to the investigator but a serious waste of time and a possible cause of image misinterpretation. Section contamination usually appears sporatically and can often be solved by changes in the fixation, embedding, or staining procedures. However, the true cause of section contamination is only occasionally identified. Four types of section contamination are described in this report along with potential causes and remedies.SURFACE CONTAMINATION is defined as any extraneous material on the surface of a section. Surface contamination occurs during the poststaining procedure and is perhaps the most common and easiest to recognize of the four section contaminations being discussed. Sections look "dirty" and the contaminating particles may be both large and dense.

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