About Us
The Bioimage Analysis Core provides cutting-edge image analysis services and support, empowering investigators to extract meaningful data from biological images. Quantitative image analysis is crucial for researchers utilizing diverse imaging techniques, including light microscopy, electron microscopy, CT, and MRI. As imaging experiments grow in scale and complexity, the demand for automated, accurate, and reproducible analysis increases. We are dedicated to meeting this need by delivering advanced image analysis solutions at the LRI.
Our team can help with the analysis of data from wide range of imaging modalities, including:
- Light Microscopy
- Brightfield Microscopy
- Fluorescence Microscopy
- Confocal & Multiphoton Microscopy
- Time-lapse Microscopy
- Whole Slide Imaging (Brightfield or Fluorescence)
- Scanning Electron Microscopy (SEM)
- Transmission Electron Microscopy (TEM)
- Small Animal Imaging (CT, MRI or luminescence)
Our team provides personalized consultation, training, and collaborative opportunities to support your image analysis needs.
If you have questions or need help, please contact Ajay Zalavadia or submit an iLab request for Bioimage Analysis.
Contacts
Services
The Bioimage Analysis Core provides a range of services to support your research needs:
Image Analysis Services
- Segmentation: Identifying and delineating structures or cells within images using both conventional and machine learning approaches.
- Pixel Classification: Identify different structures within an image
- Object Classification: Distinguishing between different types of objects (phenotype cells).
- Quantification: Measuring various parameters such as intensity, area, and volume.
- Morphometric Analysis: Analyzing the shape, size, and structure.
- Colocalization Analysis: Studying the spatial overlap of different proteins or molecules within cells.
- Spatial Analysis: Extract neighborhood information from images to study the spatial organization of biological systems or tumor microenvironments.
- 3D Reconstruction: Creating three-dimensional models from image stacks.
- Tracking: Observing and quantifying changes over time, such as cell division, cell death, migration, or angiogenesis.
- High-Content Imaging: Analyzing large datasets from high-throughput experiments to identify potential effects of various treatments on cell morphology and behavior.
- Cell behavior: Identifies various behaviors in single or multi-cell observations. Computes a range of motion and kinematics parameters for each behavior.
- Correlative Microscopy: Combining data and linking information from different imaging techniques to gain deeper insights.
Training
Our Bioimage Analysis Core is staffed by a diverse team of experts with specialized skills in life sciences, software development, and bioimage analysis. This multidisciplinary team is dedicated to supporting investigators by providing comprehensive training in fundamental image analysis techniques and developing custom solutions tailored to specific research needs. Whether you require assistance with basic image processing or advanced analytical solutions, we are here to support your research.
Beyond technical expertise, we are committed to empowering researchers through training programs designed to enhance their image analysis capabilities.
Software
Commercial Software and Tools
- Image Pro Plus 7 (Media Cybernetics)
- Image Pro 10 (Media Cybernetics)
- Image Pro 11.1 with AI Deep Learning Module (Media Cybernetics)
- Volocity 6.5 (Quorum Technologies Inc.)
- Photoshop (Adobe Inc.)
- HALO 3.2 (Indica Labs)
- InForm 3.0 (Akoya Biosciences Inc.)
- LAS-X with 3D Module (Leica Microsystem)
- Huygens Essential (Scientific Volume Imaging)
- MATLAB (MathWorks)
- BioTuring (BioTuring Inc.)
- Imaris with Cell Biology Module - limited access (Oxford Instruments)
Open-Source Software and Expertise
While we provide access to various commercial software options, our team specializes in open-source bioimage analysis tools, offering flexible and cost-effective solutions. With expertise across multiple platforms, we tailor our services to meet the unique needs of your research.
We utilize powerful open-source software such as LabGym, QuPath, ImageJ, CellProfiler, Fiji and 3D Slicer to deliver robust, reproducible image analysis. Additionally, our experts can develop and customize these tools to fit specific research requirements, enhancing the accuracy and efficiency of your experiments.
To further support researchers, we offer training programs and ongoing assistance, ensuring you can confidently use open-source tools for high-quality, reproducible analysis.
Hardware
Our Bioimage Analysis Core is equipped with state-of-the-art computing resources designed to handle the complex demands of bioimage analysis. These resources ensure efficient processing and analysis for large datasets, enabling high-quality results for your research projects. Users are able to reserve the workstations via our iLab page.
- Workstation (Ares):
- Intel Xeon 24 Core Processor
- 256GB DDR5 RAM
- Nvidia RTX A4500 20GB GPU
- Workstation (Gemini):
- Intel Core i9 12 Core Processor
- 128GB DDR4 RAM
- Nvidia RTX 3080 10GB GPU
- Workstation (Phoebe):
- Intel Xeon 24 Core Processor
- 256GB DDR5 RAM
- Nvidia Quadro M6000 24GB
- Workstation (Mercury):
- Intel Xeon 24 Core Processor
- 256GB DDR5 RAM
- Nvidia RTX A4500 20GB