SynthMT: A Synthetic Benchmark for Automated Microtubule Segmentation

Authors: Mario Koddenbrock*, Justus Westerhoff*, Dominik Fachet, Simone Reber, Felix Gers, Erik Rodner
Affiliations: HTW Berlin, BHT Berlin, MPI for Infection Biology
Project Page: https://datexis.github.io/SynthMT-project-page/ Code & Pipeline: https://github.com/ml-lab-htw/SynthMT
Paper: Synthetic Data Enables Human-Grade Microtubule Analysis with Foundation Models for Segmentation
Dataset: https://huggingface.co/datasets/HTW-KI-Werkstatt/SynthMT

*Equal contribution

🧬 Overview

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.
It provides:

• Realistic synthetic MT images
• Pixel-perfect instance segmentation labels
• A generation pipeline that adapts to any real microscope domain without the need for ground-truth annotations
• A comprehensive benchmark of classical (FIESTA), microscopy-specialized (StarDist, TARDIS, µSAM, CellSAM, Cellpose-SAM), and general-purpose foundation models (SAM, SAM2, SAM3, SAM3Text)

A core result of the associated paper:
→ SAM3Text, prompted with “thin line” and tuned on only 10 synthetic images, achieves human-grade performance on unseen real data.

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🖼 Example from the Dataset

(a) IRM-like synthetic image	(b) Ground-truth instance mask
(c) FIESTA anchor point predictions	(d) SAM3Text segmentation

** Overview of SynthMT and example predictions.**

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📦 Dataset Structure

Each sample in SynthMT contains:

Field	Type	Description
id	string	Unique image identifier
image	Image	Synthetic IRM-like image, decoded from PNG. Can be converted to a numpy array (H, W, 3) for in-memory processing.
mask	Array3D	Stack of instance masks with shape (C, 512, 512) and uint16 dtype, where C = number of instances in the image. Background pixels = 0. Stored in the dataset as a Sequence(Image()) but can be stacked in memory for in-memory pipelines.

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🧫 Biological Motivation

Microtubules (MTs) are cytoskeletal filaments essential for intracellular transport, cell motility, and mitotic spindle formation. Measuring MT count, length, and curvature is critical for in vitro reconstitution experiments, drug discovery, and mechanistic cell biology.

However:

• Manual MT annotation is time-consuming and unscalable
• IRM/TIRF imaging varies significantly across labs (domain shift)
• No large, labeled benchmarks existed for MT segmentation

SynthMT directly addresses this gap.

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📥 Installation & Loading

Install the Hugging Face datasets library:

pip install datasets

Load the dataset entirely in memory with masks stacked:

from datasets import load_dataset
import numpy as np

ds = load_dataset("HTW-KI-Werkstatt/SynthMT", split="train")

sample = ds[0]

# Image as numpy array (H, W, 3)
img_array = np.array(sample["image"].convert("RGB"))

# Masks as stacked numpy array (C, H, W)
mask_stack = np.stack([np.array(mask.convert("L")) for mask in sample["mask"]], axis=0)

No disk I/O is required — everything can be used in-memory.

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🔗 Links

• Project Page: https://datexis.github.io/SynthMT-project-page/
• Dataset: https://huggingface.co/datasets/HTW-KI-Werkstatt/SynthMT
• Code & Generation Pipeline: https://github.com/ml-lab-htw/SynthMT
• Paper: TBA

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📄 Citation

TBA

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🏷 License

CC-BY-4.0 - See LICENSE for details.

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🙏 Acknowledgements

Our work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Project-ID 528483508 - FIP 12. We would like to thank Dominik Fachet and Gil Henkin from the Reber lab for providing data, and also thank the further study participants Moritz Becker, Nathaniel Boateng, and Miguel Aguilar. The Reber lab thanks staff at the Advanced Medical Bioimaging Core Facility (Charité, Berlin) for imaging support and the Max Planck Society for funding. Furthermore, we thank Kristian Hildebrand and Chaitanya A. Athale (IISER Pune, India) and his lab for helpful discussions

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✅ **Changes made:**

1. Updated the `mask` description to reflect **stacked `(C, 512, 512)`** format.
2. Provided in-memory usage example with `numpy` stack.
3. Clarified that background = 0 and `C` = number of instances.  

This is now consistent with your **current Hugging Face dataset** setup.