Useful (but partly outdated) links
Microscopy and Imaging (commercial reference sites)
Major microscope manufacturer
- Nikon microscopyμ
An outstanding web site that offers a wealth of information on confocal microscopy, as well as on wide-field microscopy. Learn about sample preparation, aberrations, and other important aspects of confocal imaging. Based on Molecular Expressions
- nikon small world
Nikon's Small World photomicrography competition is open for everyone
- Olympus lifescience
Major microscope manufacturer
- Olympus
Olympus mircoscopy resource center. Excellent web pages on confocal microscopy, full of useful information on fluorophores, spectral bleed-through, resolution and contrast, objectives etc. Highly recommended. Based on Molecular Expressions
- Omegafilters
Optical filter manufacturer
- Omegafilters Database
An excellect tool: An interactive database of fluorophore absorption and emission spectra, along with filter set recommendations and accompanying filter spectral curves
- Perkinelmer
In vivo imaging systems for whole mice and rats (bioluminescence or fluorescence)
- Thermofisher content screening
High-Content Screening (HCS) and Analysis (HCA)
Microscopy and Imaging (non-commercial reference sites)
- ibiology
An online course covering all aspects of light microscopy in a series of video lectures
- Gensat
NINDS GENSAT BAC Transgenics Project (The Rockefeller University): The Gensat database contains a gene expression atlas of the central nervous system of the mouse based on bacterial artificial chromosomes (BACs). In each of the BAC transgenic vectors, endogenous protein coding sequences have been replaced by sequences encoding the EGFP reporter gene.
Microscopy and imaging networks
- Euro Bioimaging
Euro-BioImaging is a pan-European infrastructure project whose mission is to build a distributed imaging infrastructure across Europe that will provide open access to innovative biological and medical imaging technologies for European researchers
- ELMI
ELMI is a communication network between European scientists working in the field of light microscopy and the manufacturers. BIU is a member of ELMI.
Fluorophores and other molecular/cell biology products
- Antibodies online
An antibodies marketplace
- Takarabio
Previous Clonetech. Novel Fluorescent Proteins etc.
- Biosupplynet
CSHL Press provided web site where you can search for scientific supplies
- Cellsignal
Primary antibodies for signal transduction molecules
- Evrogen
Photoactivable fluorescent proteins etc.
- fpvis
- Mblintl
Sells CoralHue fluorescent proteins, also photochromic ones that are turned on or off on demand by exposure to different wavelenghts of light
- Sigmaaldrich
Lentiviral-based shRNA vectors for transient or stable transfection, as well as viral particle generation. The complete libraries will target 15000 human and 15000 mouse genes
- Vectorlabs
Antibodies as well as other immunohistochemistry /immunofluorescence products, labeled secondary antibodies etc.
Free imaging software
- Bioimagexd
Free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images
- Cellprofiler
CellProfiler is a free open source software designed to quantitatively measure phenotypes from thousands of images automatically
- Bio imageanalysis
Icy provides the software resources to visualize, annotate and quantify bioimaging data
- Image J
NIH program for image processing and analysis. (Windows, Mac OS 9, Mac OS X, Linux)
- Image J forum
Discussion list for ImageJ users and developers
- Image J archives
Also list archives
- Micro manager
An open source software for image acquisition. ImageJ compatible user interface. Matlab programs can be utilized in Micro-Manager. (Windows, Mac, Linux)
- epfl plugin
An ImageJ plugin for the automatic alignment of a source image or a stack to a target image
- bij isi plugin
ImageJ plugin for volume rendering by Michael D. Abramoff
- Image magick
ImageMagick is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats
- Stabilazer plugin
ImageJ plugin that corrects x-y movement of images in time-lapse image stacks
- KEGG
KEGG is a 2-D visualization tool for metabolic pathways
- Code enthought
Scientific data visualizer
- Mipav
Medical Image Processing, Analysis, and Visualization; NIH Java application that enables quantitative analysis and visualization of PET, MRI, CT, and microscopy images
- Open microscopy
OME is an open source software project to develop a database-driven system for the quantitative analysis of biological images
- Vcell
Virtual Cell software from the National Resource for Cell Analysis and Modeling allows simulation of e.g. FRAP data and membrane diffusion
- Indiana
Voxel-based real-time 3D image processing and rendering of multi-channel 3D and 4D data. (Windows, Mac OS X, Linux)
Commercial imaging software
- Leica LAS X
Leica LAS X software. Free Lite version available.
- Nikon instruments NIS
Nikon imaging software. NIS-Elements Viewer available for Windows and OS X
- Huygens
Huygens deconvolution software, also FluVR volume rendering software