Anima
Anima is an image analysis workflow platfrom built on top of Anduril. Anima acts as a superplatform for the existing imaging applications, and can run components and software written in Java, Bash (i.e. any binary), Perl, Python, R, or Matlab. In addition Anima provides API to the batch environments of Fiji, CellProfiler and ImageMagick
Microscopy and Imaging (commercial reference sites)
chroma
Optical filters - check also their resources that contain useful information about filters in general (handbook and application notes), and fluorescent protein filters (GFP catalog and application notes)
hamamatsu
CCD cameras, light sources, lasers, fibre optics etc.
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
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 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)
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 In each of the BAC transgenic vectors, endogenous protein coding sequences have been replaced by sequences encoding the EGFP reporter gene.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
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
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
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. Lite version available for Windows 7
nikon instruments NIS
Nikon imaging software. NIS-Elements Viewer available for Windows and OS X
Huygens Decon
Huygens deconvolution software, also FluVR volume rendering software