Microscopy and Image Processing Resources
- Microscope objective and filter specification sheets
- Spectra and properties of fluorescent molecules
- Image processing and analysis software
- Data Management Tips
- Online microscopy references and tutorials
Microscope Objective and Filter Specification Sheets
These sheets also list pixels sizes, which are necessary for creating scale bars and performing spatial measurements.
- Leica DM6b
- Nikon Eclipse
- Nikon TE2000 (widefield and confocal)
- Zeiss Axioskop
- Zeiss Axioscope.A1
Spectra and properties of fluorescent molecules and proteins
- FPBase Spectra Viewer (by far the best, if you ask me)
- Semrock fluorescence spectra viewer
- Molecular Probes fluorescence spectra viewer
- Fluorescent proteins properties viewer
Image processing and analysis
Guides
- Basic Image Processing with ImageJ: BEGINNERS - START HERE
- ImageJ User Guide: comprehensive reference for all basic ImageJ functions
- ImageJ Cookbook: selected basic and advanced topics
- @haesleinhuepf webinars on BioImage Analysis (mostly FIJI/ImageJ, but also CellProfiler, Python, Icy...)
- Peter Bankhead’s fluorescence microscopy in ImageJ book: basic to advanced topics, primarily geared toward fluorescence image analysis; also includes background information on nearly every topic discussed – very informative
Ethics (yes, it's something you must think about when you do any kind of image processing/analysis)
- Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images (D.W. Cromey)
- Seeing is believing? A beginners' guide to practical pitfalls in image acquisition. (A.J. North)
- Imaging methods are vastly underreported in biomedical research (Marques, Pengo, Sanders)
Software
Note that the Microscopy Facility has a stand-alone workstation with a full version of Nikon Elements and Adobe Photoshop.
- ImageJ/FIJI: Free, open-source image processing and analysis software
- We recommend installing FIJI, which is a version of ImageJ that is pre-configured with lots of useful plugins. To install FIJI, click on the correct link for your operating system and save the file anywhere convenient (except in your Program Files folder). Uncompress the downloaded file and you're ready to go! Just double-click on the fiji.app file.
- If you already have ImageJ installed, you can download the Bio-Formats Package of plugins from the Open Microscopy Environment project to allow ImageJ to open most major proprietary image formats.
- Get started using ImageJ/FIJI: check-out our basic guide.
- NIS-Elements Viewer: free, basic version of Nikon Elements
- GIMP: Free, open-source photo editing program (similar to Photoshop)
- Inkscape: Free, open-source illustration program (similar to Illustrator)
- Nyquist Calculator: online calculator to estimate the optical slice thickness and optimal step size for your instrument; will also calculate the point spread function (PSF) for your microscope.
Microscopy data management resources
- Dr. Kubow's data management tips for students
- Dr. Kubow's tips for Data Management Plans involving microscopy data
- General data management tips from the JMU Library
- Even more tips from the Stanford Library
Online microscopy references and tutorials
- The Molecular Probes Handbook: An excellent, online, searchable reference for fluorescent probes for microscopy
- Excellent general textbook on light microscopy (available online if you're at JMU): Murphy, Douglas B. and Davidson, Michael W. (2012) Fundamentals of light microscopy and electronic imaging. Wiley-Blackwell (Library Call # QH205.2 .M87 2012)
- Microscopy instructional/educational videos
- Microcourses YouTube channel
- iBiology microscopy lectures
- Microscopy educational websites
- Nikon’s MicroscopyU
- Olympus’s Microscopy Resource Center
- Zeiss Campus
- Excellent simulations from the PhET project at the University of Colorado Boulder
