Datasets:
Tasks:
Image Segmentation
Sub-tasks:
instance-segmentation
Languages:
English
Size:
1K - 10K
License:
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**Authors:** Mario Koddenbrock*, Justus Westerhoff*, Dominik Fachet, Simone Reber, Felix Gers, Erik Rodner
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**Affiliations:** HTW Berlin, BHT Berlin, MPI for Infection Biology
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**Code & Pipeline:** https://github.com/ml-lab-htw/SynthMT
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**Paper:** *Synthetic Data Enables Human-Grade Microtubule Analysis with Foundation Models for Segmentation*
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**Dataset:** https://huggingface.co/datasets/HTW-KI-Werkstatt/SynthMT
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# 🧬 Overview
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**SynthMT** is a synthetic, expert-validated dataset designed to benchmark segmentation models on *in vitro* microtubule (MT) images
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It provides:
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- Realistic **synthetic MT images**
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- Pixel-perfect **instance segmentation labels**
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- A **
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- A comprehensive benchmark of **classical
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A core result of the associated paper:
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→ **SAM3Text**, prompted with
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# 🔗 Links
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# 📄 Citation
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```bibtex
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title={TBA},
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author={TBA},
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journal={arXiv},
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year={2026}
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}
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```
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# 🙏 Acknowledgements
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```
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**Authors:** Mario Koddenbrock*, Justus Westerhoff*, Dominik Fachet, Simone Reber, Felix Gers, Erik Rodner
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**Affiliations:** HTW Berlin, BHT Berlin, MPI for Infection Biology
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**Project Page:** https://datexis.github.io/SynthMT-project-page/
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**Code & Pipeline:** https://github.com/ml-lab-htw/SynthMT
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**Paper:** *Synthetic Data Enables Human-Grade Microtubule Analysis with Foundation Models for Segmentation*
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**Dataset:** https://huggingface.co/datasets/HTW-KI-Werkstatt/SynthMT
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# 🧬 Overview
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**SynthMT** is a synthetic, expert-validated dataset designed to benchmark segmentation models on *in vitro* microtubule (MT) images visualized in interference reflection microscopy (IRM)–like conditions.
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It provides:
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- Realistic **synthetic MT images**
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- Pixel-perfect **instance segmentation labels**
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- A **generation pipeline** that adapts to any real microscope domain **without the need for ground-truth annotations**
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- A comprehensive benchmark of **classical** (FIESTA), **microscopy-specialized** (StarDist, TARDIS, µSAM, CellSAM, Cellpose-SAM), and **general-purpose foundation models** (SAM, SAM2, SAM3, SAM3Text)
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A core result of the associated paper:
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→ **SAM3Text**, prompted with “*thin line*” and tuned on **only 10 synthetic images**, achieves **human-grade performance** on unseen real data.
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# 🔗 Links
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* **Project Page:** https://datexis.github.io/SynthMT-project-page/
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* **Dataset:** https://huggingface.co/datasets/HTW-KI-Werkstatt/SynthMT
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* **Code & Generation Pipeline:** https://github.com/ml-lab-htw/SynthMT
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* **Paper:** TBA
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---
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# 📄 Citation
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```bibtex
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TBA
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```
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---
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# 🙏 Acknowledgements
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Our work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Project-ID 528483508 - FIP 12.
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We would like to thank Dominik Fachet and Gil Henkin from the Reber lab for providing data,
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and also thank the further study participants Moritz Becker, Nathaniel Boateng, and Miguel Aguilar.
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The Reber lab thanks staff at the Advanced Medical Bioimaging Core Facility (Charité, Berlin) for imaging support
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and the Max Planck Society for funding. Furthermore, we thank Kristian Hildebrand and Chaitanya A. Athale (IISER Pune, India)
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and his lab for helpful discussions
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```
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