Core Facilities

Microscopy concepts and tutorials and resources

• Molecular Expressions™ Optical Microscopy Primer, Principles and Tutorials
• Zeiss MicroImaging Campus and interactive comparison between widefield and confocal
• Carl Zeiss Laser Scanning Systems
• Nikon Microscopy U, Confocal Introduction
• Nikon Microscopy Tutorials
• University of Arizona, Cellular Imaging Core; Microscopy & Imaging Resources
• University of Helsinki, Confocal Tutorial
• Confocal Microscopy described by ER Weeks

Fluorescent Spectra databases and other tools

• University of Arizona MCB Spectra Database
• Fluorescent Protein Database
• Chroma Spectra Viewer
• Biotechne Spectra Viewer
• Molecular Probes spectra databaseFluorescence tutorials
• ThermoFisher Cell Analysis Resource Center

Sample Preparation and Techniques

• Optical considerations (coverslip thickness 1.5 optimal, NA, Refractive index matching closely, immersion, working distance of lens)
• Zeiss MicroImaging Campus has descriptions and references for many techniques such as FRET description and references, FRAP, Deconvolution, Colocalization, Fluorescent proteins
• Leica has resources for explaining several techniques in their Science Lab.
• Fluorescent Protein Poster in Nature. A user's guide by Michael Z. Lin, Atsushi Miyawaki and Roger Y. Tsien.
• Antibody resource page
• Dako Immunohistochemical Staining Methods
• Autofluorescence Causes and Cures by Wright Cell imaging facility
• Mountants and Antifades by Wright Cell imaging facility
• Online Protocols

Software

• Leica LAS-X offline software
• Zeiss ZEN lite for Windows to view Zeiss .czi and .lsm files.
• ImageJ  also for viewing .lsm files. Has plug-ins and manual or ImageJ wiki, beginner's tutorial
• Fiji ∼ Fiji Is Just Image J. a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure.
• Extensive compilation of and links to imaging software by Alembic

Digital Imaging

• Measurement: Quantitation and Colocalization
  • 39 Steps: A cautionary Tale about quantitative 3D Fluorescence Microscopy. by James Pawley
  • A guided tour into subcellular colocalization analysis in light microscopy, S. Bolte, F.P. Cordelieres Journal of Microscopy Vol 224, Issue 3, 213-232 December 2006.
  • Colocalization analysis in Fiji
• Image processing and Ethics
  • Image Processing Tutorials at Molecular Expressions
  • Extensive advice concerning image preparations and manipulations can be found in Digital Imaging Ethics written by Douglas W. Cromey
  • Guidelines on Image Manipulation Rossner and Yamada, JCB vol. 166 no. 1 11-15
  • Advice for beginning microscopist on image acquisition by Alison North JCB vol. 172 no. 1 9-18
  • Color Blind considerations when coloring your images. Examples on how to generate figures for Color-Blind: Visolve and Vischeck

Listservs

• Confocal Listserv and Archives
• Microscopy Listserv

Microscopy Courses

• Olympus link to microscopy courses
• Microscopy lecture slides from Purdue
• Teaching Material Imaging courses at INF Dresden.