# Cytoplasmic Strings Analysis in Human Embryo Time-Lapse Videos using Deep Learning Framework

arXiv: https://arxiv.org/abs/2512.09461 · HTML: https://mlsanity.com/paper/2512.09461/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 40 references that are in the map.
- First posted on arXiv 10 Dec 2025.

## Builds on (most cited first, 14 of 14)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Training data-efficient image transformers & distillation through attention](https://mlsanity.com/paper/2012.12877/) (2020)
- [What Uncertainties Do We Need in Bayesian Deep Learning for Computer Vision?](https://mlsanity.com/paper/1703.04977/) (2017)
- [DETRs Beat YOLOs on Real-time Object Detection](https://mlsanity.com/paper/2304.08069/) (2023)
- [YOLOv11: An Overview of the Key Architectural Enhancements](https://mlsanity.com/paper/2410.17725/) (2024)
- [YOLOv12: Attention-Centric Real-Time Object Detectors](https://mlsanity.com/paper/2502.12524/) (2025)
- [RT-DETRv2: Improved Baseline with Bag-of-Freebies for Real-Time Detection Transformer](https://mlsanity.com/paper/2407.17140/) (2024)
- [RF-DETR: Neural Architecture Search for Real-Time Detection Transformers](https://mlsanity.com/paper/2511.09554/) (2025)
- [EmbryosFormer: Deformable Transformer and Collaborative Encoding-Decoding for Embryos Stage Development Classification](https://mlsanity.com/paper/2210.04615/) (2022)
- [Automated Measurements of Key Morphological Features of Human Embryos for IVF](https://mlsanity.com/paper/2006.00067/) (2020)
- [Multimodal Learning for Embryo Viability Prediction in Clinical IVF](https://mlsanity.com/paper/2410.15581/) (2024)

## Abstract (arXiv)

Infertility is a major global health issue, and while in-vitro fertilization has improved treatment outcomes, embryo selection remains a critical bottleneck. Time-lapse imaging enables continuous, non-invasive monitoring of embryo development, yet most automated assessment methods rely solely on conventional morphokinetic features and overlook emerging biomarkers. Cytoplasmic Strings, thin filamentous structures connecting the inner cell mass and trophectoderm in expanded blastocysts, have been associated with faster blastocyst formation, higher blastocyst grades, and improved viability. However, CS assessment currently depends on manual visual inspection, which is labor-intensive, subjective, and severely affected by detection and subtle visual appearance. In this work, we present, to the best of our knowledge, the first computational framework for CS analysis in human IVF embryos. We first design a human-in-the-loop annotation pipeline to curate a biologically validated CS dataset from TLI videos, comprising 13,568 frames with highly sparse CS-positive instances. Building on this dataset, we propose a two-stage deep learning framework that (i) classifies CS presence at the frame level and (ii) localizes CS regions in positive cases. To address severe imbalance and feature uncertainty, we introduce the Novel Uncertainty-aware Contractive Embedding (NUCE) loss, which couples confidence-aware reweighting with an embedding contraction term to form compact, well-separated class clusters. NUCE consistently improves F1-score across five transformer backbones, while RF-DETR-based localization achieves state-of-the-art (SOTA) detection performance for thin, low-contrast CS structures. The source code will be made publicly available at: https://github.com/HamadYA/CS_Detection.