Microscopy Resources











Image Analysis and Digital Imaging 



Philosophy of Science  - and - Writing your Paper 




Useful Links



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



FPBase  -  Database for fluorescent proteins

BenchSci  -  Antibody search engine



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.