Imaging Resources

SAMPLE SUBMISSION FORMS

Whole Slide Imaging (WSI) sample submission form

SPECTRAL DATABASES

• BD Spectrum Viewer 
• Chroma  
• Fluorescent Protein Database  
• ThermoFisher Fluorescence SpectraViewer
  
  

MICROSCOPY TRAINING COURSES (GENERAL)

ANDOR/Oxford Complete Microscopy Training Course
This free course introduces concepts in detectors, fluorescence microscopy, sample preparation and confocal microscopy. Once the fundamental keystones of the course are laid, we introduce advanced microscopy applications such as TIRF, super-resolution and photostimulation techniques. Finally, we present an introduction to post-processing and image analysis tools.

iBiology Fluorescence Microscopy Course
This free online comprehensive series begins with the basics of optics, proceeds through transmitted light microscopy, covers the various methods of imaging fluorescent samples, describes how cameras work and image processing, and concludes with some of the latest advances in light microscopy. In addition to lectures, we also provide labs (filmed at a microscope) and short tips, so as to cover pragmatics of how to use microscopes.

MicroCourses from the Harvard Medical School Nikon Imaging Center
Microcourses are short educational videos on a variety of light microscopy topics, brought to you by a team of microscopists from Harvard Medical School.

Introduction to Fluorescence Light Microscopy (UNC, Pablo Ariel)
Lecture offering an introduction to terminology including contrast, resolution, widefield, and the importance of biological scales when conducting biomedical imaging studies.

Introduction to Confocal microscopy (UNC, Pablo Ariel)
Lecture introducing foundational concepts for planning and conducting biomedical research using confocal microscopy.

MYSCOPE interactive training modules for microscopy education
MyScope was developed by Microscopy Australia to provide an online learning environment for those who want to learn about microscopy. The platform provides insights into the fundamental science behind different microscopes, explores what can and cannot be measured by different systems and provides a realistic operating experience on high end microscopes.

Tutorial: guidance for quantitative confocal microscopy (Nature Protocols)
In this tutorial, the researcher is guided through all aspects of acquiring quantitative confocal microscopy images, including optimizing sample preparation for fixed and live cells, choosing the most suitable microscope for a given application and configuring the microscope parameters. Suggestions are offered for planning unbiased and rigorous confocal microscope experiments.

Educational Modules for some Image Repositories and Data Management (Global BioImaging)
Image Repositories & Data Management modules are dedicated to image data management, sharing, reuse, and image data repositories including OMERO.

LEARNING MODULES/RESOURCES:  SAMPLE PREPARATION

• Overview and Applications for Light-Sheet Microscopy (UNC, Pablo Ariel) Overview of LSFM, tissue clearing, and imaging on the UltraMicroscope II system.
• Reference protocols for tissue clearing/processing using the X-Clarity System
  • General (multi-organ, includes Antibody reference list); X-CLARITY Full Protocol, X-CLARITY_General Protocol
  • Bone-specific: Greenbaum et al 2017, X-CLARITY_BONE_Harvard
  • Brain-specific: X-CLARITY_BRAIN_Harvard

• Learn more about Logos Biosystems Deep Label antibody staining kits for LSFM imaging. Depending on demand, AMCF will purchase supplies in bulk to offer discounted pricing to individual research groups.

• Logos X-Clarity mounting solution(RIM) with representative labeling protocol
• See separate section (below) for super-resolution references and resources.
• Tutorial: guidance for quantitative confocal microscopy (Nature Protocols)

In this tutorial, the researcher is guided through all aspects of acquiring quantitative confocal microscopy images, including optimizing sample preparation for fixed and live cells, choosing the most suitable microscope for a given application and configuring the microscope parameters. Suggestions are offered for planning unbiased and rigorous confocal microscope experiments.

• Educational Modules for some Image Repositories and Data Management (Global BioImaging)

Image Repositories & Data Management modules are dedicated to image data management, sharing, reuse, and image data repositories including OMERO.

LEARNING MODULES/RESOURCES: IMAGE COLLECTION

• Zeiss Microscopy and Digital Imaging Education 
• Introduction to spectral imaging and linear unmixing (Zeiss, Learning Portal)
• Introduction to spectral unmixing (Zeiss, video tutorial)

• Modules Specific to the Zeiss 710
  • Overview of key functions, imaging configurations for Zeiss 710 (AU BioImaging, start at 20 min)
  • Setting up lambda scan/spectral imaging on Zeiss 710 (video tutorial)
  • FRET: Scanning parameters for acceptor photobleaching FRET (apFRET)
  • Photobleaching: Scanning parameters for FRAP

• Modules Specific to the Zeiss 800 with Airyscan Detection
  • Basic Principles of Airyscan Detection (Zeiss, PDF)
  • ZEISS Webinar: LSM 800 with Airyscan (YouTube)
  • Airyscan Acquisition and Processing step-by-step (Video, settings review)

• See separate section (below) for super-resolution references and resources.
  
  
• Overview and Applications for Light-Sheet Microscopy (UNC, Pablo Ariel) Overview of LSFM, tissue clearing, and imaging on the UltraMicroscope II system.
• UltraMicroscope II Users Guide (UNC, Pablo Ariel) Provides critical information regarding sample preparation, imaging parameters and expectations.

• Miltenyi Biotec training courses to learn more about sample preparation, imaging logistics, and to view some representative lightsheet fluorescence microscopy studies.
• Leica Science Lab and Microscopy Knowledge Portal  
• Nikon MicroscopyU: The Source for Microscopy Education   
• Olympus Microscopy Resource Center 
  
  

LEARNING MODULES/RESOURCES:  IMAGE ANALYSIS/VIEWERS

• IMARIS homeschool, a diverse array of training videos/tutorials for 3D, 4D image analyses. 
  • IMARIS offers several research focused applications (visualization and quantification), including educational resources for studies focused on
    • Cancer Research
    • Cell Biology
    • Developmental Biology
    • Neuroscience
  • Examples of available (free) IMARIS learning modules
    • The Basics of Quantitative Image Analysis
    • 3D/4D Image Analysis for Neuroscientists
    • Image Analysis Software for Cancer Research
    • How to Use Machine Learning and Other Object Classification Modes
    • Filament Tracer I - Detecting and Analyzing Neuron Morphology and Blood Vessels
  • Review the IMARIS User Manual

• HALO’s online learning portal (free access with UNMC email registration), user guides, technical documents, video tutorials, and webinars focused on 2D image analyses.
  • Learn more about 2D image analysis HALO modules available in the AMCF
    • Spatial Analysis
    • FISH-IF
    • Highplex Fluorescence,
    • Serial Registration Analysis
    • Tissue Classifier
  • Watch our recent Educational Webinar (12/2022) on whole slide image analyses using HALO:
    Overview and step-by-step workflow for HALO image analysis modules available in the AMCF

• Whole-Slide Image Analysis and Quantitative Pathology with QuPath (software available in AMCF core)

• Bioimage Analysis Course: The Life Cycle of an Image Data Set
  This course is designed as a graduate student level introduction to bioimage analysis and will provide an overview of the practice and principles of microscopy digital image handling. This series follows the life cycle of an image data set, from acquisition to analysis.  It teaches important concepts and best practices and provides examples that will come in handy when scientists are designing their own experiments.

• Tutorial: guidance for quantitative confocal microscopy (Nature Protocols)
  In this tutorial, the researcher is guided through all aspects of acquiring quantitative confocal microscopy images, including optimizing sample preparation for fixed and live cells, choosing the most suitable microscope for a given application and configuring the microscope parameters. Suggestions are offered for planning unbiased and rigorous confocal microscope experiments.

• Educational Modules for some Image Repositories and Data Management (Global BioImaging)
  Image Repositories & Data Management modules are dedicated to image data management, sharing, reuse, and image data repositories including OMERO.
  
  

IMAGE ANALYSIS/VIEWING

• IMARIS (core facility package available in data analysis workroom)
• IMARIS Viewer (available for anyone to download)
• HALO (selected modules available in data analysis workroom)
• NIH Image J (in data analysis workroom and available for anyone to download)
• FIJI  (in data analysis workroom and available for anyone to download)
• QuPath  (in data analysis workroom and available for anyone to download)  
• ZEN Lite (in data analysis workroom and available for anyone to download)
  
  

RESOURCES FOR SUPER RESOLUTION IMAGING

• SR imaging requires specialized sample preparation. Read the Elyra Sample Prep Guide and review educational webinar with Zeiss, below.
• Watch our recent Super Resolution Workshop with Zeiss (10/2022)
  • Part 1: Super-Resolution microscopy background concepts and theory, introduction to experiment planning, acquisition, and software basics.
  • Part 2:  Detailed discussion of acquisition software and analysis options/considerations for SIM, PALM, and STORM imaging on the Elyra PS.1.
• Single-Molecule Localization Microscopy: Theoretical Basis and Practical Guide
• Super Resolution Imaging - Sample Prep and Review Manuscripts
• Additional educational modules from Zeiss are available for AMCF researchers but cannot be posted on-line. Contact the AMCF staff to obtain access.
  
  

SUPER RESOLUTION IMAGING:  FLUORESCENT PROTEINS, DYES, BUFFERS

• Super-resolution imaging using SIM and TIRF use standard, photobleaching-resistant fluorescent proteins and dyes.  
• Super-resolution imaging using PALM/STORM requires fluorescent proteins and dyes capable of transitioning between ‘on’ and ‘off’ states.  On/Off is achieved through specific activator-reporter dye/protein pairs or when fluorophores are converted using specialized oxygen-scavenging buffers. A limited number of fluorophores may blink without specialized buffers (Alexa 647). 
• In addition to selecting appropriate fluorescent proteins and dyes, appropriate coverslips, imaging buffers, and/or mounting media must be used for successful super resolution imaging. Carefully read SIM, PALM/STORM preparation document (ElyraSamplePrepGuide). 

• Chromotek Nanobodies (novel primary and secondary antibodies for higher resolution & cleaner images) for super-resolution imaging 
• STORMreagents (a broad list of proteins, dyes, buffers, and associated references for PALM/STORM imaging from Nikon)
• ThermoFisher STORM products (list available antibody conjugates, nuclei acid stains, organelle probes, buffers and reagents for STORM imaging) 
• ThermoFisher SIM products (list of available antibody conjugates, organelle, and DNA stains)