# Open Source Infrastructure for Automatic Cell Segmentation

arXiv: https://arxiv.org/abs/2409.08163 · HTML: https://mlsanity.com/paper/2409.08163/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 16 references that are in the map.
- First posted on arXiv 12 Sep 2024.

## Builds on (most cited first, 8 of 8)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [The Importance of Skip Connections in Biomedical Image Segmentation](https://mlsanity.com/paper/1608.04117/) (2016)
- [Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm](https://mlsanity.com/paper/1906.03720/) (2019)
- [Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity](https://mlsanity.com/paper/1703.10603/) (2017)
- [FastFlows: Flow-Based Models for Molecular Graph Generation](https://mlsanity.com/paper/2201.12419/) (2022)

## Abstract (arXiv)

Automated cell segmentation is crucial for various biological and medical applications, facilitating tasks like cell counting, morphology analysis, and drug discovery. However, manual segmentation is time-consuming and prone to subjectivity, necessitating robust automated methods. This paper presents open-source infrastructure, utilizing the UNet model, a deep-learning architecture noted for its effectiveness in image segmentation tasks. This implementation is integrated into the open-source DeepChem package, enhancing accessibility and usability for researchers and practitioners. The resulting tool offers a convenient and user-friendly interface, reducing the barrier to entry for cell segmentation while maintaining high accuracy. Additionally, we benchmark this model against various datasets, demonstrating its robustness and versatility across different imaging conditions and cell types.