Classification of down-core foraminifera image sets using convolutional neural networks.

Marchant, R.; Tetard, M.; Pratiwi, A.; de Garidel-Thoron, T.

doi:10.1101/840926

Home/Archive/bioRxiv

bioRxiv · 10.1101/840926

Classification of down-core foraminifera image sets using convolutional neural networks.

Marchant, R.·Tetard, M.·Pratiwi, A.·de Garidel-Thoron, T.

View original source ↗Export metadata ↓

Abstract

Manual identification of foraminifera species or morphotypes under stereoscopic microscopes is time-consuming for the taxonomist, and a long-time goal has been automating this process to improve efficiency and repeatability. Recent advances in computation hardware have seen deep convolutional neural networks emerge as the state-of-the-art technique for image-based automated classification. Here, we describe a method for classifying large down-core foraminifera image set using convolutional neural networks. Construction of the classifier is demonstrated on the publically available endless forams image set with an best accuracy of approximately 90%. A complete down-core analysis is performed for benthic species in the Holocene period for core MD02-2518 from the North Eastern Pacific, and the relative abundances compare favourably with manual counting, showing the same signal dynamics. Using our workflow opens the way to automated paleo-reconstruction based on computer image analysis, and can be employed using our labelling and classification software ParticleTrieur.View Full Text

Source connections

Published article ↗

Explore related subjects

paleontology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Marchant, R., Tetard, M., Pratiwi, A., de Garidel-Thoron, T.. 2019-11-13. Classification of down-core foraminifera image sets using convolutional neural networks.. https://doi.org/10.1101/840926

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Constraining Palaeogeography and Palaeotides for the Cambrian using cnidarian medusae

The ocean tides influence key Earth system processes at a range of spatial and temporal scales. It is known that the geometry of ocean basins is the leading controller of tidal energetics, so well-constrained palaeogeographic reconstructions and tidal properties for Earths past are imperative when investigating other Earth system processes. Here, we present a novel way to constrain both deep-time tidal model results and reconstructions, by combining palaeoecology with sedimentology. We compare new palaeo-tidal model simulations for the Cambrian period, significant for the early origin and radiation of major animal fauna, to tidal proxies. One of the most abundant soft-bodied organisms preserved during this time are cnidarian medusae (jellyfish). A total of 17 cnidarian medusae localities were obtained through the literature, which had an adequate global distribution and occurred at regular intervals throughout the period of study. In some locations there were also estimates of palaeo-tidal range. Our results show a good agreement between the simulations and proxy data. In the few locations where there is disagreement, it is proposed that the palaeogeographic reconstructions are missing details, e.g., island chains, and our results allow for the palaeogeographic reconstructions to be improved. The proxy method presented is promising and can be applied to other time-periods with different marine fossils, particularly at evolutionary and extinction periods where the marginal marine environment is of importance.

paleontology↗

bioRxiv2019

A unique predator in a unique ecosystem: modelling the apex predator from the Late Cretaceous crocodyliform-dominated fauna in Brazil.

ABSTRACTTheropod dinosaurs were relatively scarce in the Late Cretaceous ecosystems of southeast Brazil. Instead, hypercarnivorous crocodyliforms known as baurusuchids were abundant and probably occupied the ecological role of apex predators. Baurusuchids exhibited a series of morphological adaptations hypothesised to be associated with this ecological role, but quantitative biomechanical analyses of their morphology have so far been lacking. Here, we employ a biomechanical modelling approach, applying finite element analysis (FEA) to models of the skull and mandibles of a baurusuchid specimen. This allowed us to characterise the craniomandibular apparatus of baurusuchids, as well as to compare the functional morphology of the group to that of other archosaurian carnivores, such as theropods and crocodylians. Our results support the ecological role of baurusuchids as specialised apex predators in the continental Late Cretaceous ecosystems of South America. With a relatively weak bite force (∼600 N), baurusuchids’ predation strategies likely relied on other morphological specializations, such as ziphodont dentition and strong cervical musculature. Comparative assessments of the stress distribution and magnitude of scaled models of other predators (the theropod Allosaurus fragilis and the living crocodylian Alligator mississippiensis) consistently show different responses to loadings under the same functional scenarios, suggesting distinct predatory behaviours for these animals. The unique selective pressures in the arid to semi-arid Late Cretaceous ecosystems of southeast Brazil, which were dominated by crocodyliforms, possibly drove the emergence and evolution of the biomechanical features seen in baurusuchids, which are distinct from those previously reported for other predatory taxa.View Full Text

paleontology↗

bioRxiv2019

Evolution of crab eye structures and the utility of ommatidia morphology in resolving phylogeny

ABSTRACTImage-forming compound eyes are such a valuable adaptation that similar visual systems have evolved independently across crustaceans. But if different compound eye types have evolved independently multiple times, how useful are eye structures and ommatidia morphology for resolving phylogenetic relationships? Crabs are ideal study organisms to explore these questions because they have a good fossil record extending back into the Jurassic, they possess a great variety of optical designs, and details of eye form can be compared between extant and fossil groups. True crabs, or Brachyura, have been traditionally divided into two groups based on the position of the sexual openings in males and females: the so-called ‘Podotremata’ (females bearing their sexual openings on the legs), and the Eubrachyura, or ‘higher’ true crabs (females bearing their sexual openings on the thorax). Although Eubrachyura appears to be monophyletic, the monophyly of podotreme crabs remains controversial and therefore requires exploration of new character systems. The earliest podotremous lineages share the plesiomorphic condition of ‘mirror’ reflecting superposition eyes with most shrimp, lobsters, and anomurans (false crabs and allies). The optical mechanisms of fossil and extant podotreme groups more closely related to Eubrachyura, however, are still poorly investigated. To better judge the phylogenetic utility of compound eye form, we investigated the distribution of eye types in fossil and extant podotreme crabs. Our findings suggest the plesiomorphic ‘mirror’ eyes—seen in most decapod crustaceans including the earliest true crabs—has been lost in several ‘higher’ podotremes and in eubrachyurans. We conclude that the secondary retention of larval apposition eyes has existed in eubrachyurans and some podotremes since at least the Early Cretaceous, and that the distribution of eye types among true crabs supports a paraphyletic podotreme grade, as suggested by recent molecular and morphological phylogenetic studies. We also review photoreceptor structure and visual pigment evolution, currently known in crabs exclusively from eubrachyuran representatives. These topics are critical for future expansion of research on podotremes to deeply investigate the homology of eye types across crabs.View Full Text

paleontology↗