# From Instance Segmentation to 3D Growth Trajectory Reconstruction in Planktonic Foraminifera

arXiv: https://arxiv.org/abs/2511.02142 · HTML: https://mlsanity.com/paper/2511.02142/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 61 references that are in the map.
- First posted on arXiv 4 Nov 2025.

## Builds on (most cited first, 19 of 19)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Path Aggregation Network for Instance Segmentation](https://mlsanity.com/paper/1803.01534/) (2018)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [YOLACT: Real-time Instance Segmentation](https://mlsanity.com/paper/1904.02689/) (2019)
- [Cascade R-CNN: High Quality Object Detection and Instance Segmentation](https://mlsanity.com/paper/1906.09756/) (2019)
- [Mask3D: Mask Transformer for 3D Semantic Instance Segmentation](https://mlsanity.com/paper/2210.03105/) (2022)
- [3D-SIS: 3D Semantic Instance Segmentation of RGB-D Scans](https://mlsanity.com/paper/1812.07003/) (2018)
- [SGPN: Similarity Group Proposal Network for 3D Point Cloud Instance Segmentation](https://mlsanity.com/paper/1711.08588/) (2017)
- [Hierarchical Aggregation for 3D Instance Segmentation](https://mlsanity.com/paper/2108.02350/) (2021)
- [TensorMask: A Foundation for Dense Object Segmentation](https://mlsanity.com/paper/1903.12174/) (2019)
- [A Survey on Instance Segmentation: State of the art](https://mlsanity.com/paper/2007.00047/) (2020)
- [Deep Watershed Transform for Instance Segmentation](https://mlsanity.com/paper/1611.08303/) (2016)
- [InstanceCut: from Edges to Instances with MultiCut](https://mlsanity.com/paper/1611.08272/) (2016)
- [An Exploration of 2D and 3D Deep Learning Techniques for Cardiac MR Image Segmentation](https://mlsanity.com/paper/1709.04496/) (2017)
- [GASP, a generalized framework for agglomerative clustering of signed graphs and its application to Instance Segmentation](https://mlsanity.com/paper/1906.11713/) (2019)

## Abstract (arXiv)

Planktonic foraminifera, marine protists characterized by their intricate chambered shells, serve as valuable indicators of past and present environmental conditions. Understanding their chamber growth trajectory provides crucial insights into organismal development and ecological adaptation under changing environments. However, automated tracing of chamber growth from imaging data remains largely unexplored, with existing approaches relying heavily on manual segmentation of each chamber, which is time-consuming and subjective. In this study, we propose an end-to-end pipeline that integrates instance segmentation, a computer vision technique not extensively explored in foraminifera, with a dedicated chamber ordering algorithm to automatically reconstruct three-dimensional growth trajectories from high-resolution computed tomography scans. We quantitatively and qualitatively evaluate multiple instance segmentation methods, each optimized for distinct spatial features of the chambers, and examine their downstream influence on growth-order reconstruction accuracy. Experimental results on expert-annotated datasets demonstrate that the proposed pipeline substantially reduces manual effort while maintaining biologically meaningful accuracy. Although segmentation models exhibit under-segmentation in smaller chambers due to reduced voxel fidelity and subtle inter-chamber connectivity, the chamber-ordering algorithm remains robust, achieving consistent reconstruction of developmental trajectories even under partial segmentation. This work provides the first fully automated and reproducible pipeline for digital foraminiferal growth analysis, establishing a foundation for large-scale, data-driven ecological studies.