Biomedisa
Introduction to Biomedisa
Biomedisa is a free and easy-to-use open-source application designed for segmenting large 3D volumetric images, such as CT and MRI scans. Developed at The Australian National University's Computational Biology and Medical Imaging Lab (CTLab), Biomedisa offers a powerful tool for researchers and clinicians to analyze complex biological and medical images with high precision and efficiency.
Biomedisa represents a significant advancement in the field of biomedical image segmentation. Its combination of smart interpolation, deep learning capabilities, and user-friendly design makes it a valuable tool for researchers and clinicians alike. By providing accurate and efficient segmentation of large 3D volumetric images, Biomedisa contributes to the advancement of biomedical research and clinical practice.
Key Features and Capabilities
Smart Interpolation: Biomedisa employs smart interpolation of sparsely pre-segmented slices, enabling accurate semi-automated segmentation. This method considers the complete underlying image data, ensuring high-quality results even with minimal manual input.
Deep Learning Integration: The application supports deep learning for fully automated segmentation across similar samples and structures. Users can train Biomedisa's deep neural network using their own datasets, enhancing the accuracy and speed of segmentation tasks.
Compatibility and Integration: Biomedisa is compatible with popular segmentation tools like Amira/Avizo, ImageJ/Fiji, and 3D Slicer. This compatibility allows users to seamlessly integrate Biomedisa into their existing workflows, leveraging the strengths of multiple tools for comprehensive image analysis.
Applications and Use Cases
Biomedical Research: Biomedisa has been successfully used in various biomedical research projects, including the analysis of mouse molar teeth from micro-CT scans and mitochondria in electron microscopy images. The application's deep learning features have also been employed to analyze large datasets, such as 187 bee brains, revealing minor but statistically significant variations.
Clinical Applications: In clinical settings, Biomedisa can assist in the segmentation of medical images, aiding in the diagnosis and treatment planning of various conditions. Its user-friendly interface and powerful algorithms make it accessible to clinicians without extensive computational expertise.
Accessibility and Ease of Use
Web-Based Platform: Biomedisa is accessible through a web browser, eliminating the need for complex software installations or configurations. This accessibility makes it an ideal tool for researchers and clinicians who require a straightforward and efficient image segmentation solution.
Community and Support: The Biomedisa community provides resources and support for users, including tutorials, webinars, and a YouTube channel with instructional videos. These resources help users get started with the application and maximize its potential for their specific needs.
Resources used
Publications
Introducing Biomedisa as an open-source online platform for biomedical image segmentation
Lösel P, van de Kamp T, Jayme A, Ershov A, Faragó T, Pichler O, Tan Jerome N, Aadepu N, Bremer S, Chilingaryan S, Heethoff M, Kopmann A, Odar J, Schmelzle S, Zuber M, Wittbrodt J, Baumbach T, Heuveline V - Nature Communications - 2020
