Literature
Microscopy
- Fluorescence microscopy - avoiding the pitfalls. - Journal of Cell Science, 2007
- Designing a rigorous microscopy experiment: Validating methods and avoiding bias. - Journal of Cell Biology, 2020
- Tutorial: guidance for quantitative confocal microscopy. - Nature Protocols, 2020
Super-resolution
- The cell biologist's guide to super-resolution microscopy - Journal of Cell Science, 2020
Image Analysis and Digital Imaging
- Digital Images Are Data: And Should Be Treated as Such - Douglas W. Cromey, Methods Mol Biol. 2013
- Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images - Douglas W. Cromey, Science and Engineering Ethics 2010
- The 39 Steps: A Cautionary Tale of Quantitative 3-D Fluorescence Microscopy - Jim Pawley, Biotechniques, 2000
Philosophy of Science - and - Writing your Paper
- Strong Inference - J. Platt, Science, 1964
- Paradigms Lost and Paradigms Found: Examples of Science Extraordinary and Science Pathological – And How To Tell the Difference - N.J. Turro, Angew. Chem. Int. Ed., 2000
- Whitesides' group: Writing a paper - G.M. Whitesides, Advanced Materials, 2004
- Point of view: Tell me a story - J.R. Sanes, eLife 2019
Useful Links
Software
ImageJ / FIJI - Open source image analysis software - download and extensive tutorials
Leica LAS X - Free 90-day license, full version
Zeiss's ZEN Blue - Free 90-day license, version of (Windows only)
SVI Huygens - Free test license
Databases
FPBase - Database for fluorescent proteins
BenchSci - Antibody search engine
Imaging
Leica Tips - Leica YouTube channel with short instructional videos on widefield microscopy, software, and imaging
Microforum - Forum focused on hardware, acquisition, and specimen-related aspects of scientific imaging
Image Analysis
Images.sc - Image analysis forum
Color Universal Design - Figure design friendly to colorblind people
Online Classes, Courses, and Tutorials
Microcourses - Instructional videos on light microscopy from the Nikon Imaging Center at Harvard Medical School
iBiology Microscopy Series - Comprehensive video series about light microscopy, from basic optics, imaging, to image analysis.
Imaris - Online tutorials
Introduction to R - Full course from Alex Douglas and Thomas Cornulier, University of Aberdeen
Nikon - Online resources for microscopy education
Zeiss Campus - Educational online resources for microscopy
Operating the Microscope and Imaging Topics
Kölhler Illumination
Aligning transmitted light illumination optics very time you use the microscope for a brightfield imaging technique. Here is how and why.
Microscope resolution, Rayleigh and Nyquist criteria for sample - iBiology video lecture.
Sampling density and Nyquist rate - choosing the right pixel size for your acquisition.