Sie sind hier: Startseite Links of Interest Microscopy and Image Analysis

Microscopy and Image Analysis

General References

Molecular Expressions Optical Microscopy Primer - a great microscopy resource which discusses many aspects of microscopy in an understandable fashion. Their virtual microscopes are informative, as well as fun.

Olympus FluoView Confocal Microscopy Resource Center - information about confocal microscopy, and digital imaging as well as interactive tutorials.

Nikon MicroscopyU - Another useful resource for information on confocal as well as general microscopy.

Microscopy and Imaging Resources - Extensive index from the University of Arizona Microscopy Alliance, which also contains an index for confocal microscopy.

Archives of the Confocal Listserver - Searchable archives from the Confocal e-mail user's group.

Assay Guidance Manual - eBook from the NCBI which covers development of assays for HCS/HTS, but also useful for smaller scale assays. 

Spectra

Spectra Viewer from Fluorofinder is useful in that it is manufacturer-independent

Spectraviewer from the folks at the Imaging Facility of the MPI for Brain Research in Frankfurt.

Fluorescence Spectraviewer from ThermoFisher/eBioscience (formerly Molecular Probes).

Fluorescence Spectrum Viewer from Becton Dickinson.

Fluorescent Protein Resource Center - in addition to excitation/emission maxima it contains other useful information about fluorescent proteins and their properties.

Fluorophores.org - comprehensive database with useful spectral library.

Open Source Software / Freeware

Imaris - Lighthouse has a license for Imaris, the premier commercial 3D-analysis software. There are numerous tutorials and help files available on the company website. The company also makes a free version of the software, Imaris Viewer, available for download.

ImageJ -Sophisticated Java-based freeware program which is able to run on any platform and is available from the National Institutes of Health allowing post-acquisition processing and analysis of confocal images, image stacks and much more.

A good site with tips for how to get started using ImageJ is the ImageJ Tutorials page, as well as the searchable archives of the ImageJ Listserv and the ImageJ Documentation page.

Fiji - a useful image processing program derived from ImageJ, with most of the microscopy-specific plugins already included.

CellProfiler and CellProfiler Analyst - open source HCS image analysis software available from the Broad Institute.

QuPath - open source software for whole slide image analysis, developed by Peter Bankhead at Queen's University, Belfast. Once you have your slide scanned, this is the place to start for spatial analysis and phenotyping.

CytoMAP - open source software from the Gerner lab at the University of Washington. CytoMAP is designed to extract quantitative information on cellular localization and composition within tissue regions. After QuPath, this would be the next step for spatial phenotyping.

 

Microscopy Networks and Societies

German BioImaging (GerBi - GMB) - Homepage of the German Bioimaging society. Lighthouse is a part of German BioImaging.

MIAP - Homepage of the Microscopy and Image Analysis Platform, a regional network of microscopy and image analysis facilities and units. Lighthouse is a partner unit of MIAP, and the MIAP website includes an overview of all of the MIAP partner units.

Antibody Directories

Linscott's Directory - Directory of commercially available antibodies.

Antikoerper Online - Directory of commercially available antibodies

Company Sites

Carl Zeiss website - where you can download the free Zen LITE digital imaging software, a useful Windows-based freeware program you can use to help with examination of your brightfield, widefield fluorescence, and confocal images.

Olympus/Evident website - where you can get more information about the scanR Screening Station and its powerful analysis software.

Akoya Biosciences - for more information about spatial biology and the Akoya Phenocycler Fusion (CODEX) system.

Leica Microsystems - where you can get more information about the SP8 spectral confocal microscope.