Microscopy

What We Do

The Microscopy Service operates as two multi-user facilities in which our skilled staff provides training and assistance in the use of advanced light microscopy instrumentation and image processing software while also providing full-service imaging. We work closely with investigators to support their optical imaging needs and offer in-depth consultation for how our instrumentation and services can be best leveraged in their research. Consultations include, but are not limited to, experimental design, selecting appropriate microscopy methods and instruments, optimizing image acquisition, data delivery, and data analysis using open-source and commercial software. Additionally, we perform high-resolution whole-slide scanning of tissue sections that have undergone histological or fluorescence staining to support projects such as mouse phenotyping and disease status assessment.

As a collaborative effort with JAX Data Science, we also work on integrating image processing, image analysis, and AI-based workflows into an institution-wide web platform, JAX Image Tools.

Support services

• In-depth training sessions
• General consultation for all professional levels (student interns, pre-docs, post-docs, research scientists, and faculty)
• Guidance on experimental design using all basic and advanced microscopy instruments
• Full service histological and fluorescence whole-slide scanning and data delivery

Modes of microscopy

• Widefield light and fluorescence: upright, and inverted live-cell
• Standard confocal
• Spinning disk confocal
• Fluorescence lifetime imaging (FLIM)
• Super-resolution confocal
• Multiphoton
• Light sheet
• High-content screening using Opera Phenix
• Laser-capture microdissection
• Second harmonic generation-based imaging and collagen quantification

Image processing

• Extended-depth-of-field image stack processing
• Software for image deconvolution
• Custom CellProfiler/Ilastik pipelines for high-throughput image analysis and automation
• Generation and annotation of data sets for AI training
• Software support and user training for Bitplane Imaris, SVI Huygens, Cellpose, CellProfiler, QuPath, etc.
• Design of and consultation on AI-based workflows for deep-learning networks and inference from large 2D images
• Design of and consultation on AI-based workflows for deep-learning networks and inference from large 2D images

Project Spotlight:  

JAX Image Tools, a web tool suite and graphical interface, allows the integration of image processing, image analysis, and AI-based workflows into an institution-wide web-based platform. JAX Image Tools is a fruitful collaborative effort between Microscopy Service and JAX Data Science and the tool has been used by multiple JAX investigators and JMCRS.