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Links & Downloads

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:

Biology resources:

Microscopy techniques - Colocalization:

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:

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