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.
- 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:
- 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.
- Image Processing and Analysis in ImageJ and ImageJ Macro Programming - very nicely and detailed written Textbooks by Kota Miura.
- The ImageJ Macro Language Reference Documentation
- 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.
The Wiki pages of the Imaging Core Facility (Authentication required, available to Unibasel-members only)