Unravelling the 3D microarchitecture of Nannoconus Micaliths : From Synchrotron Imaging to Python-Based Modelling

Scientific background
Among extinct calcareous nannoplankton, Nannoconus was the major carbonate producer in Early Cretaceous marine environments ( 152–120 Ma)¹. Its relatively large size ( 5–20 μm) and high skeletal mass ( 200–1,400 pg²˒³) make this genus particularly significant in terms of marine carbonate production. Over more than 30 million years, Nannoconus skeletons contributed to extensive carbonate accumulations on the seafloor, potentially influencing seawater chemistry and the global carbon cycle.
The Nannoconus skeleton is composed of an assemblage of micaliths, the individual building units of the skeleton⁴. Each micalith consists of imbricated calcite components, and different Nannoconus species are characterized by distinct micalith morphologies. However, the internal microstructure of these building units had not previously been resolved at a scale suitable for investigating their biomineralization mechanisms.
By combining X-ray ptychographic computed tomography (PXCT) performed on the SWING beamline at the SOLEIL synchrotron with scanning electron microscopy (SEM), we recently obtained the first three-dimensional reconstruction of a Nannoconus micalith at nanometric resolution⁵. This reconstruction revealed a highly hierarchical architecture (Fig. 1), comprising 12 segments formed by the spiral stacking of calcite lamellae with two distinct, alternating inclinations (hereafter referred to as lamellae A and B). The micalith also features a wall surrounding a central canal whose radius gradually varies from the base to the apex.
This complex architecture raises questions about the mechanisms governing calcification and structural organization. In particular, it is consistent with a model of biologically controlled mineralization in which organic matrices may have guided the orientation and arrangement of the calcite lamellae.

Research objectives
The initial three-dimensional reconstruction was based on a single micalith, and its structural features were subsequently extrapolated to other Nannoconus morphologies. Although these results demonstrate the potential of PXCT for investigating nannofossil biomineralization, analysing additional specimens from different species and geological intervals is essential to determine whether the observed features are consistent across individuals and taxa.
PXCT data have already been acquired for five additional micaliths belonging to different Nannoconus species. For each specimen, preliminary segmentations of the calcite lamellae, together with corresponding electron-density maps and mass estimates, are available. However, these datasets have not yet been fully analysed, partly because high-resolution image reconstruction and segmentation are time-consuming.
The main objective of this Master 2 internship is to investigate the three-dimensional architecture of these five micaliths using image processing, geometric reconstruction and Python-based modelling.
The project will address two main tasks :
1. Image processing and segmentation : Improve the visualization and segmentation of the calcite lamellae in the five micaliths using Dragonfly 3D visualization software at Institut Néel. The aim is to obtain more detailed and consistent representations of their internal architecture.
2. Three-dimensional reconstruction and geometric modelling : Reconstruct the three-dimensional shape of each micalith using a Python-based code published alongside the initial study. Building on the workflow established in that study, the intern will characterize individual lamellae and quantify key geometric parameters, including radius, length, inclination, tilt and azimuth (Fig. 1).
Comparative analysis of these parameters across specimens will help identify the geometric features that govern the organization and potential structural stability of micaliths. It will also provide a basis for assessing the variability of their architecture across species and for investigating possible constraints on their biomineralization.

Methods and expected outcomes
The internship will combine three-dimensional visualization and segmentation of synchrotron PXCT datasets with computational geometry and Python-based modelling. The intern will build on an existing, step-by-step and reproducible workflow developed in the initial study, with opportunities to refine image processing, automate geometric measurements and compare the reconstructed structures across specimens.
The expected outcomes include improved three-dimensional reconstructions of five Nannoconus micaliths, a quantitative characterization of their geometric properties, and an assessment of similarities and differences in their internal architecture. These results will help establish whether the structural features identified in the first specimen are representative of a broader range of Nannoconus morphologies and provide new insights into the geometric constraints associated with their calcification.

Candidate profile
We are looking for a motivated Master 2 student with a background in Earth sciences or a related discipline, an interest in paleontology and a strong curiosity for image processing, three-dimensional modelling and scientific computing.
Applicants should have a degree in a field related to paleontology, mineralogy, geosciences or environmental physics. Previous experience with image processing, 3D visualization software or physical characterization techniques is essential. An interest in Python programming and quantitative approaches is highly desirable.
The internship offers an opportunity to work at the interface of paleontology, mineralogy, synchrotron imaging and computational modelling, using existing experimental datasets to address fundamental questions about the structure and formation of an extinct marine calcifier.

References
1Bown, P.R. 2005. Cenozoic calcareous nannofossil biostratigraphy, ODP Leg 198 Site 1208 738 (Shatsky Rise, northwest Pacific Ocean). Proceedings of the Ocean Drilling Program, scientific results, 739 : 1–44. College Station, TX (Ocean Drilling Program).
2Tremolada F, Young, J. 2002. Volume calculation of Cretaceous calcareous nannofossils. Journal of Nannoplankton Research, 24(3) : 199–202.
3Chowdhury, R. 2025. Chemical and physical characterization of Nannoconus, the main planktonic 750 bio-producer of carbonates in the cretaceous seas : insights into biomineralization processes. Thesis. Université Grenoble Alpes (France). https://theses.hal.science/tel-05080049
4Aubry, M-P, 2025. Biomineralization in the Calcareous Nannoplankton Phenotypic Expressions Across Life Cycles, Geometric Control on Diversification, and Origin. Minerals, 15 (3) : 322. https://doi.org/10.3390/min15030322
5Chowdhury R., Boudjehem R., Suchéras-Marx B., Dupraz M., Kulow A., da Silva JC., Hazemann J-L., Aubry M-P., Pérez J., Fernandez-Martinez A., Giraud F. 2026a. The 3D submicron-scale skeletal reconstruction of Nannoconus (Cretaceous calcareous nannofossil) - Insights on biomineralization. Biogeosciences, 23 : 2023–2043. https://doi.org/10.5194/bg-23-2

Figure 1. Successive steps followed in the 3D reconstruction of a Nannoconus micalith6. (a) Micalith of Nannoconus globulus as seen in scanning electron microscopy ; black dashed lines individualize the segments visible in this image. (b) Tomographic image obtained from the PXCT analysis of N. globulus with the wall and central canal ; a calcite lamella is marked in red. (c) Segmented calcite lamella obtained from PXCT data ; the resolution is on the order of 40 nanometers. (d) Reconstruction of a segment with alternating, properly oriented, lamella-A (yellow) and -B (green). (e) Three-dimensional reconstruction of a N. globulus micalith ; longitudinal (top) and basal (bottom) views show it to be composed of 12 (re)constructed segments ; two successive segments are labeled S1 and S2, respectively.