General Information:

Before you start: Microscopy pitfalls:

http://jcb.rupress.org/content/172/1/9.full

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

http://jcb.rupress.org/content/166/1/11.full

Sample preparation:

https://microscopy.duke.edu/guides/intro-sample-prep-immunofluorescence

http://www.ihcworld.com/_protocols/general_ICC/fixation.htm

Mounting media:

Mounting media: An overview

Autofluorescence:

Autofluorescence: Causes and Cures

Fluorochrome Table:

http://www.sciencegateway.org/resources/fae1.htm

Spectra Viewer:

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cell-Analysis/Labeling-Chemistry/Fluorescence-SpectraViewer.html

SVI Nyquist Calculator:

http://www.svi.nl/NyquistCalculator

General introduction to image analysis and automation in microscopy:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791844/

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

http://microscopy.fsu.edu/primer/index.html
http://www.microscopyu.com/
https://www.olympus-lifescience.com/en/microscope-resource/
http://www.olympusconfocal.com/theory/index.html
http://zeiss-campus.magnet.fsu.edu/
http://www.invitrogen.com/site/us/en/home/support/Tutorials.html
http://www.mikroskopie.de/ (German)

Software:

Fiji: https://fiji.sc/ 

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: www.irfanview.net

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:

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:

http://www.youtube.com/watch?v=KoqpCsha-UU

Cellprofiler on youtube:

http://www.youtube.com/results?search_query=cell+profiler&oq=cell+profiler&gs_l=youtube.3..0i10.204.2362.0.2515.13.13.0.0.0.0.115.1023.12j1.13.0...0.0...1ac.1.11.youtube.9-z6nDNvBkw

Imaris tutorials:

https://imaris.oxinst.com/tutorials

Introduction to confocal microscopy, Kurt Thorn:

http://www.youtube.com/user/ibioseminars/videos?query=microscopy

Introduction to fluorescence microscopy, Nico Sturman:

http://www.youtube.com/watch?list=SPAAAAED3D1EA9E4E1&feature=player_detailpage&v=iPrZ84kHH2U

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

http://www.youtube.com/watch?feature=player_detailpage&v=FPCqvdsnJwQ

http://www.youtube.com/watch?feature=player_detailpage&v=bhjP9PqfJRE

http://www.youtube.com/watch?feature=player_detailpage&v=Bom9d-Knz0w

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

http://www.youtube.com/watch?feature=player_detailpage&v=w2Qo__sppcI

http://www.youtube.com/watch?feature=player_detailpage&v=DPGijjVTncs

http://www.youtube.com/watch?v=2NssL7RWmjc