Automated Classification of Pectinodon Bakkeri Teeth Images Using Machine Learning

Microfossil dinosaur teeth are studied by paleontologists in order to better under- stand dinosaurs. Currently, tooth classification is a long, manual, error-ridden process. Deep learning offers a solution that allows for an automated way of classifying images of these microfossil teeth. In this thesis, we aimed to use deep learning in order to develop an automated approach for classifying images of Pectinodon bakkeri teeth. The proposed model was trained using a custom topology and it classified the images based on clusters created via K-Means. The model had an accuracy of 71%, a precision of 71%, a recall of 70.5%, and an F1-score of 70.5%

Identifying microbial life in rocks: Insights from population morphometry

The identification of cellular life in the rock record is problematic, since microbial life forms, and particularly bacteria, lack sufficient morphologic complexity to be effectively distinguished from certain abiogenic features in rocks. Examples include organic pore-fillings, hydrocarbon-containing fluid inclusions, organic coatings on exfoliated crystals and biomimetic mineral aggregates (biomorphs). This has led to the interpretation and re-interpretation of individual microstructures in the rock record. The morphologic description of entire populations of microstructures, however, may provide support for distinguishing between preserved micro-organisms and abiogenic objects. Here, we present a statistical approach based on quantitative morphological description of populations of microstructures. Images of modern microbial populations were compared to images of two relevant types of abiogenic microstructures: interstitial spaces and silica–carbonate biomorphs. For the populations of these three systems, the size, circularity, and solidity of individual particles were calculated. Subsequently, the mean/SD, skewness, and kurtosis of the statistical distributions of these parameters were established. This allowed the qualitative and quantitative comparison of distributions in these three systems. In addition, the fractal dimension and lacunarity of the populations were determined. In total, 11 parameters, independent of absolute size or shape, were used to characterize each population of microstructures. Using discriminant analysis with parameter subsets, it was found that size and shape distributions are typically sufficient to discriminate populations of biologic and abiogenic microstructures. Analysis of ancient, yet unambiguously biologic, samples (1.0 Ga Angmaat Formation, Baffin Island, Canada) suggests that taphonomic effects can alter morphometric characteristics and complicate image analysis; therefore, a wider range of microfossil assemblages should be studied in the future before automated analyses can be developed. In general, however, it is clear from our results that there is great potential for morphometric descriptions of populations in the context of life recognition in rocks, either on Earth or on extraterrestrial bodies.This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Program (grant agreement no. 646894 to MVZ) and under the ERC Seventh Framework Programme FP7/2007- 2013 (grant agreement no. 340863 to JMG-R). JMG-R also acknowledges the Ministerio de Economía y Competitividad of Spain through the project CGL2016-78971-P. We are grateful to seven anonymous reviewers for their helpful comments. We thank four anonymous reviewers for their useful comments which greatly improved a previous version of the manuscript. This is IPGP contribution n°4098

A Federated Computational Workflow for Analysis of DISKOS Digital Palynological Slides

A novel federated computational workflow for analyzing digital palynological slide images is implemented in this thesis. The slide data files, typically exceeding 3GB, present significant data mobility and computation challenges. The novel distributed computational framework is implemented to address privacy concerns and the challenges associated with moving large data. The idea is to move computational to the data location, optimally utilizing local computational capacity and reducing data movement. Trained deep-learning models deployed in a containerized environment leveraging the Docker technology are integrated in the workflow with a user-friendly interface, and users can run processes with the trained models. The workflow processes include reading slide image files, generating tiled images, and identifying and removing undesirable tiles such as blank tiles. Object detection with the watershed segmentation algorithm identifies tiles with potential microfossils. The identified dinoflagellates are classified with a trained convolution neural network (CNN) model. The classification results are sent to the host and shared with the users. The federated computational approach effectively addresses the challenges related to moving and handling large palynological slide images, creating a more efficient, scalable, and distributed pipeline. Collaborative efforts involving domain experts for model training with more annotated slide images will improve the effectiveness of the workflow

A Federated Computational Workflow for Analysis of DISKOS Digital Palynological Slides.

A novel federated computational workflow for analyzing digital palynological slide images is implemented in this thesis. The slide data files, typically exceeding 3GB, present significant data mobility and computation challenges. The novel distributed computational framework is implemented to address privacy concerns and the challenges associated with moving large data. The idea is to move computational to the data location, optimally utilizing local computational capacity and reducing data movement. Trained deep-learning models deployed in a containerized environment leveraging the Docker technology are integrated in the workflow with a user-friendly interface, and users can run processes with the trained models.\\ The workflow processes include reading slide image files, generating tiled images, and identifying and removing undesirable tiles such as blank tiles. Object detection with the watershed segmentation algorithm identifies tiles with potential microfossils. The identified dinoflagellates are classified with a trained convolution neural network (CNN) model. The classification results are sent to the host and shared with the users. The federated computational approach effectively addresses the challenges related to moving and handling large palynological slide images, creating a more efficient, scalable, and distributed pipeline. Collaborative efforts involving domain experts for model training with more annotated slide images will improve the effectiveness of the workflow

Silhouette-based gait recognition using Procrustes shape analysis and elliptic Fourier descriptors

This paper presents a gait recognition method which combines spatio-temporal motion characteristics, statistical and physical parameters (referred to as STM-SPP) of a human subject for its classification by analysing shape of the subject's silhouette contours using Procrustes shape analysis (PSA) and elliptic Fourier descriptors (EFDs). STM-SPP uses spatio-temporal gait characteristics and physical parameters of human body to resolve similar dissimilarity scores between probe and gallery sequences obtained by PSA. A part-based shape analysis using EFDs is also introduced to achieve robustness against carrying conditions. The classification results by PSA and EFDs are combined, resolving tie in ranking using contour matching based on Hu moments. Experimental results show STM-SPP outperforms several silhouette-based gait recognition methods

Microstructures in Metasedimentary Rocks from the Neoproterozoic Bonahaven Formation, Scotland: Microconcretions, Impact Spherules, or Microfossils?

Microscopic spherules in relatively undeformed mudstones of the Neoproterozoic Bonahaven Formation, Islay, Scotland, are differentiated from their matrix by a sharp micron-scale, smoothly rounded boundary. These elongate spherules were earlier interpreted as hollow bodies filled penecontemporaneously by glauconite and subsequently metamorphosed to phengite, but their origin remains a matter of debate. Spherules observed in thin section are predominantly rounded (∼74%) but can exhibit a flat edge or protrusion at one end. In 11% of a sample population, two or more spherules are conjoined. X-ray diffraction indicates that spherule-bearing mudstones consist mainly of muscovite, with variable amounts of kaolin-group minerals and minor iron-chlorites. A range of physical origins for the spherules – including microconcretions or metamorphic microstructures; deposition from the sky as micrometeorites, microtektites/microkrystites, or accretionary volcanic ash particles; and detrital grains – is considered but rejected on distributional, morphological, and mineralogical evidence. Biological origins are considered most likely, especially protistan tests similar to the vase-shaped microfossils found in somewhat older Neoproterozoic rocks. If correct, this provides the first report of eukaryotic life in the Dalradian succession that passes critical tests for biogenicity and new evidence for testate microfossils in post-Sturtian but pre-Marinoan aged rocks.Earth and Planetary SciencesOrganismic and Evolutionary Biolog

Cyanobacteria and the Great Oxidation Event:Evidence from genes and fossils

This article is corrected by:Errata: Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils Volume 58, Issue 5, 935–936, Article first published online: 14 August 2015International audienceCyanobacteria are among the most ancient of evolutionary lineages, oxygenic photosynthesizers that may have originated before 3.0 Ga, as evidenced by free oxygen levels. Throughout the Precambrian, cyanobacteria were one of the most important drivers of biological innovations, strongly impacting early Earth's environments. At the end of the Archean Eon, they were responsible for the rapid oxygena-tion of Earth's atmosphere during an episode referred to as the Great Oxidation Event (GOE). However, little is known about the origin and diversity of early cyanobacterial taxa, due to: (1) the scarceness of Precambrian fossil deposits; (2) limited characteristics for the identification of taxa; and (3) the poor preservation of ancient microfossils. Previous studies based on 16S rRNA have suggested that the origin of multi-cellularity within cyanobacteria might have been associated with the GOE. However, single-gene analyses have limitations, particularly for deep branches. We reconstructed the evolutionary history of cyanobacteria using genome scale data and re-evaluated the Precambrian fossil record to get more precise calibrations for a relaxed clock analysis. For the phylogenomic reconstructions, we identified 756 conserved gene sequences in 65 cyanobacterial taxa, of which eight genomes have been sequenced in this study. Character state reconstructions based on maximum likelihood and Bayesian phylogenetic inference confirm previous findings, of an ancient multicellular cyanobacterial lineage ancestral to the majority of modern cyanobacteria. Relaxed clock analyses provide firm support for an origin of cyanobacteria in the Archean and a transition to multicellularity before the GOE. It is likely that multicellu-larity had a greater impact on cyanobacterial fitness and thus abundance, than previously assumed. Multicellularity, as a major evolutionary innovation, forming a novel unit for selection to act upon, may have served to overcome evolutionary constraints and enabled diversification of the variety of mor-photypes seen in cyanobacteria today

Fungal spores as palaeoenvironmental indicators of anthropogenic activity

Fungal spores often occur in palynological preparations and have been successfully incorporated in both biostratigraphic and palaeoenvironmental investigations. However, the majority of palynologists choose to ignore such microfossils, primarily because of the difficulties relating to their identification. Where they have been used conventional palynological extraction procedures have been implemented in the preparation of samples. The suitability of such techniques for the recovery of fungal palynomorphs has been assumed in many cases.The objectives of this thesis were to study the effect of different processing techniques on the recovery of fungal palynomorphs, to propose a suitable morphological recording system and to investigate the potential of using fungal palynomorphs as palaeoenvironmental indicators of anthropogenic activity.Following the specification of a suitable extraction procedure for fungal palynomorphs and an appropriate morphological recording system 215 types were described. These types were encountered in samples from modern and archaeological situations and across a variety of different environments. The types fall into 19 morphological categories as defined in the recording system. Many of the types are restricted to either modern or archaeological sample sets although some are common to both. 96 types are comparable to known fungal taxa, 8 are considered algal in origin, 4 are parasite eggs and 1 has been identified as a rhizopod species. The remaining 106 can only be classified morphologically until they can be related to known taxa.Although an objective was to employ the Comparative Approach and use the palynomorph assemblages from known modem environments in the palaeoenvironmental interpretation of the archaeological material, it was not feasible. This is principally because of the limited overlap of taxa between modern and archaeological samples and is most likely a reflection of the restricted range of material considered. However, this approach demonstrates a promising future, subject to more extensive sampling regimes.Palaeoenvironmental interpretation of the archaeological samples was possible using the Indicator Species Approach. The results support and often enhance other forms of palaeoenvironmental analysis and in no instance were contra- indications encounteredThis success testifies to the importance of fungal palynology and the need for continuing research in this area

Upper Cretaceous radiolaria from the Atlantic Ocean and Cyprus

Micropalaeontological analyses, with special reference to radiolaria, have been carried out on 255 samples of Campanian - Maastrichtian sediments from 3 sections encountered at offshore DSDP/IPOD Sites in the Atlantic Ocean and 20 onshore sections in Cyprus in the Mediterranean sea. Radiolarian assemblages recorded here are integrated with calcareous nannofossils where possible, the studied sections having been carefully chosen in order to test existing biostratigraphical schemes using radiolaria and calcareous microfossils. Of the published zonation schemes for the Late Cretaceous, seven are discussed and their application to material recorded here considered. A number of interesting biostratigraphical observations confirmations and conclusions have been made in relation to the geological history of Cyprus, whilst the radiolarian biostratigraphical database from DSDP Sites 152 and 369A has been amended. A taxonomic atlas has been compiled, with extensive synonymy lists and the geographical and stratigraphical occurrence patterns both for published species and for new forms recorded exclusively in this study. The stratigraphical occurrences recorded here are correlated with co-occurring calcareous nannofossils. The taxonomic atlas includes 141 taxa and 47 genera which are described and/or figured. Of these morphotypes, 59 are left in open nomenclature, many of which represent new and undescribed species to be formally described when their occurrence patterns are fully researched. Eighty-two of the species recorded have published ranges which include the Campanian whilst the ranges of a further 11 species are here extended into the (stratigraphically higher) Campanian stage. Published radiolarian ranges are confirmed and extended. The organisation and storage of the lithological and micropalaeontological data from this study on a computer database allowed for rapid searches for correlative and inversely correlative sample characteristics. Equally, future rapid selection of samples for purposes such as refining zonation schemes or selection of particularly well-preserved specimens for photography or specific reappraisal is facilitated. Controls on production and preservation of siliceous microfossils are discussed and applied to the interpreted depositional conditions in the Late Cretaceous. The effects of these controls, as interpreted for the Late Cretaceous, are discussed in relation to biostratigraphical utilization of the group. A comprehensive assessment of sample processing and analytical techniques and a discussion on the technical problems encountered, together with their impact on recorded data, is included. Finally, future research areas have been defined in relation to the following : 1. developing/refining radiolarian biozonation; 2. standardization of preparation techniques, data production and storage; 3. advancement of stored computerised data to include pictorial representation of taxa; 4. more extensive work on Cyprus involving correlation with DSDP/ODP material

Ceramic composition at Chalcolithic Shiqmim, northern Negev desert, Israel: investigating technology and provenance using thin section petrography, instrumental geochemistry and calcareous nannofossils

Technological innovations in ceramic production and other crafts are hallmarks of the Chalcolithic period (4500–3600 BCE) in the southern Levant, but details of manufacturing traditions have not been fully investigated using the range of analytical methods currently available. This paper presents results of a compositional study of 51 sherds of ceramic churns and other pottery types from the Chalcolithic site of Shiqmim in the northern Negev desert. By applying complementary thin section petrography, instrumental geochemistry and calcareous nannofossil analyses, connections between the raw materials, clay paste recipes and vessel forms of the selected ceramic samples are explored and documented. The study indicates that steps in ceramic manufacturing can be related to both technological choices and local geology. Detailed reporting of the resulting data facilitates future comparative ceramic compositional research that is needed as a basis for testable regional syntheses and to better resolve networks of trade/exchange and social group movement