EMSeek Dataset Overview

Background

The EMSeek dataset accompanies the paper Bridging Electron Microscopy and Materials Analysis with an Autonomous Agentic Platform (Chen et al., 2025). It supports the system’s reference-guided, single-click segmentation workflows and provides curated examples for downstream lattice reconstruction, property prediction, and literature-grounded reasoning. The collection spans atomic-resolution and nanoscale transmission electron microscopy scenarios so that SegMentor, EM2CIF, MatProphet, and related agents can be trained and evaluated on a unified benchmark of heterogeneous materials tasks.

Directory Layout

Task-specific data are organized at the repository root:

atom_columns/
atomic_defects/
metal_alloy_defects/
nanoparticles/
single_atom_catalysts/
README.md

Each task directory contains one folder per material or specimen. Inside every material folder the files follow a consistent structure:

task/material/
├── image/ # Raw microscopy frames (.png)
├── label/ # Pixel-wise masks (.png)
├── bbox/ # YOLO-style annotations (.txt)
└── prompt.txt # Optional textual prompt (one-word / concise / detailed)

prompt.txt exists for all current materials except atomic_defects/WSe2.

Task Coverage

Atomic Column Segmentation (atom_columns)

• Materials: DyScO3, LiCoO2, MoS2, NiO, Pt, Si, SrTiO3, graphene.
• 13,356 image/label/bbox triplets; all images are 256×256 grayscale.
• Labels are stored as RGB PNGs but are binary (two colors).
• Bounding boxes mark atomic-column centroids for detection.

Atomic Defect Identification (atomic_defects/WSe2)

• 107 grayscale images at 1024×1024 resolution.
• RGB masks use three colors (background plus two defect-related classes).
• Bounding boxes highlight each defect center; no prompt file in this task.

Metal Alloy Defects (metal_alloy_defects/FeCrAl)

• 182 images (174 at 1024×1024, 8 at 2048×2048) with matching bboxes.
• 183 grayscale labels (one extra label file without a matching image).
• Prompts summarize defect characteristics for language-aware agents.

Nanoparticle Analysis (nanoparticles)

• Materials: Au@C, Au@Ge, Au@SiN, Au@zeolite, CdSe@C, Fe3O4, Fe3O4@SiO2, Pd@C, PtSn@Al2O3.
• 822 images; 821 labels/bboxes (one missing label/bbox for Au@C).
• Image sizes vary from 1002×668 up to 4096×4096; 1024×1024 and 2048×2048 are common.
• Labels are mostly binary grayscale PNGs, with a small number stored as RGB/RGBA.

Single-Atom Catalysts (single_atom_catalysts/Pt@NC)

• 25 grayscale images (512×512, 1024×1024, and 2048×2048).
• RGB masks are binary (two colors), with matching bboxes and promp
  

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