Microscopy in general:

• A short overview of milestones in light microscopy in chronological order.
• Optical Microscopy Primer - Zeiss Campus - On these two webpages you can find everything about microscopy, including very useful Java tutorials.
• iBiology Microscopy Courses (by UCSF and Howard Hughes Medical)
  Two online Microscopy courses (one long, one short) that are freely available, and consist of ~30 min. lectures on all major topics in light microscopy given by leaders in the field, labs demonstrating specific techniques at the microscope, and short tips.
• Confocal Principles - the key principles of confocal microscopy on one page.
• Confocal Microscopy List - forum of discussion about a wide-variety of topics related to microscopy. 
• Microforum - a more recent forum to discuss specimen, hardware and acquisition aspects of scientific imaging
• iScopeCalc - online tool designed for configuring microscopes to achieve nyquist sampling and optimal field of view.

Antibodies, fluorescence dyes, fluorescent proteins, filters:

• BenchSci - A.I. Driven Antibody Search
• Fluorescence spectra viewers:
  • FPbase - a database of fluorescent proteins.
  • SearchLight (Semrock)
  • Fluorescence SpectraViewer - Plot and compare spectra and check the spectral compatibility for many fluorophores.
  • Table of Fluorochromes @ Iowa State University - check for excitation and emission maxima of most of the current fluorochromes.
• Fluorescent Biosensor Database - Repository of genetically encodable fluorescent biosensors.

Biology resources:

• The Human Protein Atlas - Database of proteins' distribution in cells, tissues and organs.
• Allen Brain Map - Brain atlases and advanced tools for neurobiologists.
• Image Data Resource (IDR) - Public repository of image datasets from published scientific studies.
• BioNumbers - Search tool for molecular biology associated numbers 

Microscopy techniques - Colocalization:

• "Dr. Bob's tutorial on colocalization" - A really nice tutorial explaining colocalization on only 10 pages.
• Costes et al. 2004 - The paper describing the algorithm underlying many actual colocalization plugins/programs.
• JACoP (Just Another Colocalization Plugin) - To our knowledge still best ImageJ-Plugin currently available for colocalization analysis. You will find some info on this plugin on the Image documentation Wiki and in this review: Bolte & Cordelières 2006.

Downloads - Fiji, ImageJ and Icy:

• Icy - Icy provides the software resources to visualize, annotate and quantify bioimaging data. It has a very intuitive user interface, provides a huge amount of plugins for specific tasks, is scriptable with Python and JavaScript and ships with an easy-to-understand graphical "programming" toolbox.
• Fiji (ImageJ) - A distribution of ImageJ aimed for Life Sciences. Fiji bundles ImageJ, Java, Java 3D and a lot of plugins organized into a coherent menu structure to facilitate the installation process for the end user. Additionally, it has an automatic update function that not only keeps your ImageJ up-to-date, but also takes care of Plugins etc.
• IMCF Update Site for Fiji - Additional Fiji macros and plugins provided by the IMCF.
• The complete ImageJ user guide - a very extensive and comprehensive manual on all the details of ImageJ.
• The ImageJ Macro Language Reference Documentation

Image analysis:

• Image.sc forum - focusing on software-oriented aspects of scientific imaging, particularly image analysis, processing, acquisition, storage, and management of digital scientific images.
• 'Image Processing and Analysis for Life Scientists' MOOC (Massive Open Online Course) by the BioImaging & Optics Platform of the EPFL.
• Image Processing and Analysis in ImageJ and ImageJ Macro Programming - very nicely and detailed written Textbooks by Kota Miura.
• Robert Haase has his own bio-image analysis group in Dresden. On top of developing great tools for the community, he loves teaching and sharing his teaching materials. We can strongly recommend:
  • His in depth general introduction to bio-image analysis youtube channel
  • His in depth introduction to Bio-image_Analysis_with_Python. This GitHub repo contains slides and notebooks for practical examples.
  • Finally you'll find here a very thorough list of additional ressources
• NEUBIAS is the Network of european bioimage analysts. Since 2020 they started to record online teachings of howtos for tasks in the context of a specific tools. You can find these videos here: youtube channel link
• Pete Bankhead is the head of the BioImage Analysis and Digital Pathology group in Edinburgh and the original developer of QuPath and also wrote an amazing book about Introduction to Bioimage Analysis

IMCF-Wiki
The Wiki pages of the Imaging Core Facility (Authentication required, available to Unibasel-members only)