Guidelines how to report your microscopy data in publications:

1. A guide to accurate reporting in digital image acquisition – can anyone replicate your microscopy data? Heddleston, J.M., Aaron, J.S., Khuon, S., Chew, T.-L. (2021)J. Cell Sci. doi: 10.1242/jcs.254144,(link)
2. A guide to accurate reporting in digital image processing – can anyone reproduce your quantitative analysis? Aaron, J.S., Chew, T.-L. (2021) J. Cell Sci. doi:10.1242/jcs.254151,(link)

Books:

1. Handbook of Biological Confocal Microscopy 
2. Bioimage Data Analysis
3. Fundamentals of Light Microscopy and Electronic Imaging

Tutorials and guides on microscopy for beginners and advanced users:

1. "Tutorial: guidance for quantitative confocal microscopy", Nature Protocols volume 15, pages1585–1611(2020).  DOI: 10.1038/s41596-020-0313-9
2. "A beginner’s guide to rigor and reproducibility in fluorescence imaging experiments", Molecular Biology of the CellVol. 29, No. 13. doi.org/10.1091/mbc.E17-05-0276 
3. Neubias getaway 
4. Intro videos of OiVM - Optical Imaging & Vital Microscopy

Online courses:

1. List of online courses: www.gerbi-gmb.de/onlinetraining
2. Microcourses: background knowledge
3. Bioimage analysis course Lecture BioImage Analysis 2020

Image analysis:

1. Guide through the bio-image analysissoftware universe
2. Neubias Academy
3. Youtube channel of Neubias with webinars
4. Amira online hands-on
5. Huygens webinars
6. Image analysis forum, where you can ask disturbing questions: forum.image.sc
7. Reproducible image handling and analysis Kota Miura and Simon F Nørrelykke. www.embopress.org/doi/full/10.15252/embj.2020105889

Microscopy forums:

1. www.microlist.org

Fluorophores list:

1. Fluorophores list www.fluorophores.tugraz.at/substance/
2. Another Fluorophores list searchlight.semrock.com
3. List of dyes and filter match www.spectra.arizona.edu (enable flash player)
4. www.chroma.com/spectra-viewer

Online materials provided by microscope companies

1. Nikon  www.microscopyu.com
2. Olympus www.olympus-lifescience.com/en/microscope-resource/
3. Leica www.leica-microsystems.com/science-lab/
4. Zeiss zeiss-campus.magnet.fsu.edu/index.html