Tissue Images Dataset (tissue_images_dataset)

Overview

This DeepTrackAI repository provides a copy of the Segmented anisotropic ssTEM dataset of neural tissue, a dataset of serial section Transmission Electron Microscopy (ssTEM) prepared for training and evaluating image segmentation methods.

The content mirrors the public dataset by Gerhard et al., available from both the Original GitHub repository and figshare (DOI: 10.6084/m9.figshare.856713).

The dataset contains 2 stacks of ssTEM images of the Drosophila melanogaster third instar larva ventral nerve cord. Each stack consists of 20 serial sections. The imaged volume measures approximately 4.7 × 4.7 × 1 μm³, with a voxel resolution of 4.6 × 4.6 × 45–50 nm³.

Summary

• Number of stacks: 2 (1 training, 1 test)
• Sections per stack: 20 (40 total)
• Image size: 1024 × 1024 pixels
• Image format: 8-bit grayscale TIFF
• Labels: For each class, binary images; for multi-class segmentation, 8-bit images with pixel values encoding structure type (see table below).

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Original Source

• Title: Segmented anisotropic ssTEM dataset of neural tissue
• Authors: Stephan Gerhard, Jan Funke, Julien Martel, Albert Cardona, Richard Fetter
• Sources:
  • Original GitHub repository
  • figshare (DOI: 10.6084/m9.figshare.856713)
• Licenses:
  • Original GitHub repository: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)
  • figshare: Creative Commons Attribution 4.0 International (CC BY 4.0

If you use this dataset in your research, please follow the licensing requirements and properly attribute the original authors.

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Dataset Structure

/tissue_images_dataset
├── stack1/                     # Training stack 
│   ├── raw/                    # Raw ssTEM images
│   │   ├── 00.png  
│   │   ├── 01.png  
│   │   └── ... 
│   ├── membranes/              # Binary segmentation masks: membranes 
│   │   ├── 00.png  
│   │   ├── 01.png  
│   │   └── ... 
│   ├── mitochondria/           # Binary segmentation masks: mitochondria 
│   │   ├── 00.png  
│   │   ├── 01.png  
│   │   └── ... 
│   ├── synapses/               # Binary segmentation masks: synapses 
│   │   ├── 00.png  
│   │   ├── 01.png  
│   │   └── ... 
│   └── labels/                 # Multi-class segmentation masks 
│       ├── labels00000000.png  
│       ├── labels00000001.png  
│       └── ... 
└── stack2/                     # Test stack 
    └── raw/                    # Raw ssTEM images
        ├── 00.png  
        ├── 01.png  
        └── ... 

Each filename is a sequential numerical identifier, consistent across raw and segmentation folders. In the labels/ directory, each pixel is assigned one of the following values:

Value	Structure
0	Membrane (0°)
32	Membrane (45°)
64	Membrane (90°)
96	Membrane (135°)
128	Membrane junction
159	Glia / Extracellular
191	Mitochondria
223	Synapse
255	Intracellular

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How to Access the Data

Clone the Repository

git clone https://github.com/DeepTrackAI/tissue_images_dataset
cd tissue_images_dataset

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Attribution

If you use this dataset, please cite the Segmented anisotropic ssTEM dataset of neural tissue.

Cite the dataset:

Gerhard S, Funke J, Martel J, Cardona A, Fetter R. Segmented anisotropic ssTEM dataset of neural tissue. figshare. Dataset (2013). DOI: 10.6084/m9.figshare.856713

@misc{gerhard2013sstem,
  title        = {Segmented anisotropic ssTEM dataset of neural tissue},
  author       = {Gerhard, Stephan and Funke, Jan and Martel, Julien and Cardona, Albert and Fetter, Richard},
  howpublished = {figshare},
  year         = {2013},
  doi          = {10.6084/m9.figshare.856713}
}

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License

Note: The original dataset is distributed under two different licenses depending on the source:

• CC BY-NC-SA 3.0 via the GitHub repository
• CC BY 4.0 via figshare

This replication dataset is shared under the more restrictive license, the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0) License, consistent with the original GitHub repository.