bbbc-datasets 0.1.6

PyTorch-compatible dataset manager for BBBC datasets

BBBC Segmentation Datasets (2D/3D) - A PyTorch Dataset Manager

📌 Overview

This package provides a PyTorch-compatible dataset manager for Broad Bioimage Benchmark Collection (BBBC) datasets.

It allows users to:

• Download and manage BBBC segmentation datasets automatically
• Load datasets as PyTorch Dataset objects
• Handle 2D & 3D images properly
• Support image augmentations via torchvision.transforms (#TODO)

🚀 Installation

Install from PyPI

pip install bbbc-datasets

Install from Source

Clone the Repository

git clone https://github.com/mario-koddenbrock/bbbc_datasets.git
cd bbbc_datasets

Install Dependencies

pip install -r requirements.txt

Dependencies:

• torch, torchvision (Deep Learning Framework)
• numpy, tifffile, opencv-python (Image Handling)
• requests, matplotlib (Downloading & Visualization)

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📂 Available Datasets

You can list all available BBBC datasets without downloading them. You can also filter the datasets to show only 2D, only 3D, or both types of datasets.

from examples.load_dataset import list_available_datasets

# List all datasets
list_available_datasets()

# List only 2D datasets
list_available_datasets(filter_3d=False)

# List only 3D datasets
list_available_datasets(filter_3d=True)

Output

📂 Available BBBC Datasets:
- BBBC003: DIC microscopy images of mouse embryos for segmentation analysis.
- BBBC004: Synthetic fluorescence microscopy images of nuclei with varying clustering probabilities.
- BBBC005: Simulated fluorescence microscopy images with varying focus blur.
- BBBC006: Z-stack fluorescence microscopy images of human U2OS cells.
- BBBC008: Dataset: Fluorescence microscopy images of human HT29 colon cancer cells.
- BBBC010: Live/dead assay of C. elegans exposed to pathogens.
- BBBC024: 3D Synthetic HL60 Cell Line Images with Varying Clustering Probability and SNR.
- BBBC027: 3D Synthetic Colon Tissue Images with Varying SNR.
- BBBC028: Polymerized Structures in Differential Interference Contrast (DIC) Microscopy.
- BBBC029: Synthetic Differential Interference Contrast (DIC) Images.
- BBBC032: 3D Mouse Embryo Blastocyst Cells.
- BBBC033: 3D Mouse Trophoblast Stem Cells.
- BBBC034: 3D Induced Pluripotent Human Stem Cells (hiPSC).
- BBBC035: Simulated HL60 Cells from the Cell Tracking Challenge.
- BBBC038: Kaggle 2018 Data Science Bowl - Nuclei Segmentation.
- BBBC039: Nuclei of U2OS Cells in a Chemical Screen.
- BBBC046: FiloData3D - Synthetic 3D Time-Lapse Imaging of A549 Cells with Filopodia.
- BBBC050: Nuclei of Mouse Embryonic Cells.

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🎨 Visualizing Dataset Samples

Display First Image from Each Dataset

Requires downloading datasets first!

You can display samples from the datasets. Similar to listing datasets, you can filter the samples to show only 2D, only 3D, or both types of datasets.

from examples.load_dataset import display_dataset_samples

# Display samples from all datasets
display_dataset_samples()

# Display samples from only 2D datasets
display_dataset_samples(filter_3d=False)

# Display samples from only 3D datasets
display_dataset_samples(filter_3d=True)

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📥 Download and Load a Dataset

Load a Dataset as a PyTorch Dataset

from bbbc_datasets.datasets.bbbc004 import BBBC004
from torch.utils.data import DataLoader

# Load BBBC004 dataset
dataset = BBBC004()

# Create a DataLoader
dataloader = DataLoader(dataset, batch_size=4, shuffle=True)

# Iterate through data
for images, labels in dataloader:
    print(f"Batch shape: {images.shape}, Labels: {labels.shape if labels is not None else 'None'}")

The filter_datasets function allows you to filter a list of dataset classes based on whether they are 2D, 3D, or both.

from bbbc_datasets.utils.general import filter_datasets
from tests import DATASETS

# Filter all datasets
datasets_all = filter_datasets(DATASETS)

# Filter only 2D datasets
datasets_2d = filter_datasets(DATASETS, filter_3d=False)

# Filter only 3D datasets
datasets_3d = filter_datasets(DATASETS, filter_3d=True)

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🛠 Running Tests

Validate Dataset URLs

Checks if all dataset URLs are reachable 🌍

python -m unittest tests/test_dataset_urls.py

Verify Dataset Loading

Ensures datasets can be loaded and accessed correctly 🛠

python -m unittest tests/test_dataset_loading.py

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📝 Up-next

• Thinking of what is up next
• Maybe integrating other datasets as cellpose, livecell, etc.

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🙌 Contributing

Contributions are welcome! If you find issues or want to add new features, feel free to:

• Submit a Pull Request
• Report Issues in the GitHub Issues section

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📜 License

This project is licensed under the MIT License.