Training and Resources
The AMCF has several training resources available for researchers. Please select from the following to go to that section of this page:
- Image Analysis/Viewing Software
- Spectral Databases for Fluorophore Selection
- Grant/Proposal Writing Resources
- Instrument-Specific Resources
- Vendor-Led Microscopy Learning Modules
- General Microscopy Courses
- Recent AMCF Publications
Imaging Software
The following software may be helpful to view and analyze your images. Most are available to use in the AMCF Data Analysis Workroom (DRC I Rm 1036), and some are free to download for your own usage.
Spectral Databases for Fluorophore Selection
- ThermoFisher Fluorescence SpectraViewer
- BD Spectrum Viewer
- Chroma Spectra Viewer
- Fluorescent Protein Database
Grant/Proposal Writing Resources, Forms
- Full Data Management & Sharing Plan
- AMCF Funding Acknowledgement
- AMCF Reproducibility and Rigor Policy
- AMCF Instrument Summary
- Data Analysis Workroom Terms of Use Agreement
- OMERO Server Access Form
- Whole Slide Imaging (WSI) Sample Submission Form
Instrument-Specific Resources
Click on the instrument or workstation below to learn about its resources:
Zeiss Elyra PS.1 Super Resolution Microscope
- Instrument specifications can be found on the AMCF Instrument Page
- 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 (Elyra Sample Prep Guide).
- Single-Molecule Localization Microscopy: Theoretical Basis and Practical Guide
- Nikon: Single-Molecule Super-Resolution Imaging
- Watch our Super Resolution Workshops with Zeiss (10/2022)
- Antibodies and Reagents
- 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)
- Additional Super Resolution educational resources are available for AMCF researchers. Contact the AMCF to request access.
Zeiss 800 LSM with Airyscan for High Resolution Imaging
- Instrument specifications can be found on the AMCF Instrument Page
- Basic Principles of Airyscan Detection (Zeiss, PDF)
- ZEISS Webinar: LSM 800 with Airyscan (YouTube)
- Airyscan Acquisition and Processing: step-by-step and settings review (YouTube)
Zeiss 710 Confocal Laser Scanning Microscope
- Instrument specifications can be found on the AMCF Instrument Page
- Overview of key functions, imaging configurations for Zeiss 710 (AU BioImaging, start at 20 min)
- Introduction to spectral imaging and linear unmixing (Zeiss Learning Portal)
- Introduction to spectral unmixing (YouTube)
- Setting up lambda scan/spectral imaging on Zeiss 710 (YouTube)
- FRET: Scanning parameters for acceptor photobleaching FRET (YouTube)
- Photobleaching: Scanning parameters for FRAP (YouTube)
Zeiss Cell Discoverer 7
- Instrument specifications can be found on the AMCF Instrument Page
- Overview of System Features (YouTube)
Zeiss Axioscan 7 Whole Slide Imaging System
- Instrument specifications can be found on the AMCF Instrument Page
- Researchers must complete Whole Slide Imaging (WSI) sample submission form prior to submitting samples for imaging.
- In the notes section, indicate reference locations for setting collection parameters for individual channels within/across slides, if needed.
- Watch our HALO Overview & Step-by-step Workflow webinar on whole slide image analyses using HALO.
- For analysis module details, see the HALO section just below.
- Whole-Slide Image Analysis and Quantitative Pathology with QuPath (available in AMCF core)
Miltenyi Biotec Ultramicroscope II Light Sheet Fluorescence Microscope
- Instrument specifications can be found on the AMCF Instrument Page
- Samples must be secured (spiked holder, or super glued) sample base for imaging. Small samples (i.e. zebrafish) should be embedded in 0.5 - 2% low temperature melting agarose (Sigma Aldrich A9414) prior to mounting/imaging. Consult with AMCF prior to scheduling your imaging session.
- Reference protocols for tissue clearing/processing using the X-Clarity System:
- General (multi-organ, includes Antibody reference list): X-CLARITY Full Protocol and X-CLARITY General Protocol
- Bone-specific: Greenbaum et al 2017 and X-CLARITY BONE Protocol (Harvard)
- Brain-specific: X-CLARITY BRAIN Protocol (Harvard)
- AMCF SOP: XClarity Tissue Clearing Researcher Guide
- Overview and Applications for Light-Sheet Microscopy (YouTube) Overview of LSFM, tissue clearing, and imaging; seminar presented by Pablo Ariel, UNC.
- Watch on-demand Miltenyi Biotec training courses to learn more about sample preparation, imaging logistics, and to view some representative studies.
- Learn more about Logos Biosystems DeepLabel antibody staining kits for LSFM imaging. Depending on demand, AMCF will purchase supplies in bulk to offer discounted pricing to individual research groups.
- X-Clarity is a de-lipidation process, dense tissues with low lipid content may not become completely transparent.
- Cleared samples may be stored in PBS (will cause some temporary whitening) post clearing but must be fully infiltrated in refractive index matching media (RIM) > 24h prior to imaging.
- Logos X-Clarity mounting solution (RIM) with representative labeling protocol.
- Researchers should minimize sample sizes to facilitate successful tissue clearing and efficiently manage resultant volumetric image file sizes (10’s to 100’s of GBs).
- ImSpector software on the ultramicroscope performs limited visualization, see AMCF’s working with images post LSFM imaging document.
- LSFM is relatively low-resolution imaging in large volumes, higher resolution (≥ 0.25 um x,y, ≥ 0.5 um z) can be obtained in the UNMC Multiphoton Intravital & Tissue Imaging Core.
HALO Image Analysis Workstation
- Learn more about 2D image analysis HALO modules available in the AMCF
- Spatial Analysis, FISH-IF, Highplex Fluorescence, Serial Registration Analysis, Tissue Classifier, Microglial Activation Fluorescence Module
- Review the Data Analysis Workroom Terms of Use Agreement
- Watch AMCF training webinars with vendor specialists
- HALO Overview & Step-by-step Workflow on whole slide image analyses
- HALO Microglia Activation Module workflow
- RNAscope labeling and analysis using HALO
- Visit HALO’s online learning portal (free access with UNMC email registration) to access user guides, technical documents, video tutorials, and webinars. Michael Tomac is the UNMC point of contact.
- Try a free online demo with HALO, simply upload 1-3 images and await your results.
IMARIS Image Analysis Workstation
- Review the Data Analysis Workroom Terms of Use Agreement
- Cancer Research: Imaris for Cancer Research includes a variety of spatial interaction measurements, such as: distribution of objects around a Surface, shortest distance, volume overlap and nearest neighbor analysis. Imaris offers unique segmentation/object detection tools (like Spots and Surfaces) to better visualize and understand the sample in 3D.
- Cell Biology: Imaris for Cell Biologists provides the functionality for smart cell-based segmentation, analysis on a per cell basis and discovery of intracellular relationships. The package includes automated tracking, detection of cell division and creation of interactive lineage trees along with statistical tests and a two-way interface for customization in Matlab, Java or Python.
- Developmental Biology: Featuring state of the art volume rendering, plus object detection and tracking tools Imaris for Tracking is perfect for researchers who want to automatically analyze moving objects including those that divide over time, create a lineage tree plot and generate quantitative information from their image data.
- Neuroscience: Enables 3D reconstruction of neurons and arborization analysis. It can resolve various structures, such as axons and dendrites, somas, dendritic spines, microglia, or astrocytes. It calculates a range of neuron-specific measurements, such as dendrite or segment length, orientation, diameter, branch level, spine density and spine shape analysis and classification. This is also perfect for tracing blood vessels and getting measurements like segment length and total length, diameter, mean segment intensity and orientation of segments.
- Visit IMARIS homeschool to find a diverse array of training videos/tutorials.
- Review the IMARIS User Manual
- Imaris Viewer is a free 3D/4D microscopy image viewer for viewing raw images. Share images, take your high performance Imaris renderings wherever you go. Imaris Viewer works with over 40 microscopy file types, including Tiff.
Vendor-Led Microscopy Learning Modules
- Zeiss Microscopy and Digital Imaging Education
- ANDOR/Oxford Complete Microscopy Training Course
- Leica Science Lab and Microscopy Knowledge Portal
- Nikon MicroscopyU: The Source for Microscopy Education
- Olympus Microscopy Resource Center
General Microscopy Courses
- Image Repositories & Data Management Overview
These educational modules focus on image data management, including sharing, reuse, and the use of image data repositories like OMERO. Presented by Global BioImaging. - iBiology Fluorescence Microscopy Course
This comprehensive online series covers optics, transmitted light, fluorescent sample imaging, camera function, image processing, and advanced light microscopy, including practical lab sessions. - Introduction to Confocal Microscopy
This YouTube lecture recording introduces foundational concepts for planning and conducting biomedical research using confocal microscopy. Presented by Pablo Ariel, UNC. - Introduction to Fluorescence Light Microscopy
This YouTube lecture recording introduces key terminology like contrast, resolution, and widefield microscopy, emphasizing the importance of biological scales in biomedical imaging. Presented by Pablo Ariel, UNC. - MicroCourses
This YouTube channel features short educational videos covering a variety of light microscopy topics. Presented by microscopists from Harvard Medical School's Nikon Imaging Center. - Microtutor
This interactive platform offers self-paced virtual light microscopy education for early-career scientists, covering fundamental principles and practical experimental information. - MyScope
These interactive training modules provide an online learning environment to understand the fundamental science behind different microscopes, their measurement capabilities, and offer realistic operating experience. Presented by Microscopy Australia. - Tutorial: Guidance for quantitative confocal microscopy
This tutorial, published in Nature Protocols, guides researchers through acquiring quantitative confocal microscopy images, covering sample preparation, microscope selection, configuration, and planning rigorous experiments.
Recent AMCF Publications
AMCF users are obligated to fully acknowledge the facility and its funding sources in formal publications and presentations containing any data generated in the facility.
- Appropriately citing the AMCF helps us maintain internal and external funding allowing us to minimize hourly core usage fees.
View a listing of recent publications from researchers who generated data with assistance of the AMCF.