Links & Downloads

General Information:
Before you start: Microscopy pitfalls:

Before you publish: Ethics and data manipulation, from JCB:

Sample preparation:

Mounting media:

Mounting media: An overview


Autofluorescence: Causes and Cures

Fluorochrome Table:

Spectra Viewer:

SVI Nyquist Calculator:

General introduction to image analysis and automation in microscopy:

The following websites offer comprehensive learning for all aspects of microscopy and are a great resource: (German)



Fiji is an image processing package.

It can be described as a distribution of ImageJ together with Java, Java 3D and a lot of plugins organized into a coherent menu structure.


IrfanView is a very fast, small, compact and innovative freeware (for non-commercial use) graphic viewer. (For PC only)

It contains a nice batch conversion (with image processing) to change picture formats and sizes. (e.g. tiff to jpg)


Automator is a tool that is already included in the MAC operating system. It can also be used for batch conversion and for much more.


Video Tutorials:
ImageJ tutorials on youtube:

Cellprofiler on youtube:

Imaris tutorials:

Introduction to confocal microscopy, Kurt Thorn:

Introduction to fluorescence microscopy, Nico Sturman:

Introduction to live cell, photoactivation, bleaching and super resolution, Jennifer Lippincott-Schwartz:

Introduction to super resolution imaging, Xiaowei Zhuang, Stefan Hell: