Useful links to web sites.
Links 2
http://www.nightsea.com/sfa-sharing/fluorescence-spectra-viewers/
- Link list for many fluorescence spectra viewers
- If you don't find a particular spectra on one viewer, try another
- 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)
- CCD cameras, light sources, lasers, fibre optics etc.
- Special microscopy slides
http://www.leica-microsystems.com/home/
- Major microscope manufacturer
https://www.mattek.com/product-category/cultureware/
- Glass bottom culture dishes for live cell imaging
https://www.nikoninstruments.com/en_EU/
- Major microscope manufacturer
- https://www.nikoninstruments.com/en_EU/Learn-Explore/Techniques
- Nice visual presentations on microscopy techniques
- https://www.microscopyu.com/
- 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.
- http://www.nikonsmallworld.com/
- Nikon's Small World photomicrography competition is open for everyone
https://www.olympus-lifescience.com/en/
- Major microscope manufacturer
- http://olympus.magnet.fsu.edu/
- 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
- Optical filter manufacturer
- http://www.omegafilters.com/curvomatic/
- An excellect tool: An interactive database of fluorophore absorption and emission spectra, along with filter set recommendations and accompanying filter spectral curves
http://www.perkinelmer.com/category/in-vivo-imaging
- In vivo imaging systems for whole mice and rats (bioluminescence or fluorescence)
- High-Content Screening (HCS) and Analysis (HCA)
- http://www.thermofisher.com/fi/en/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html
- Fluorescence SpectraViewer
https://www.zeiss.fi/microscopy/home.html
- Major microscope manufacturer
https://www.ibiology.org/ibioeducation/taking-courses/ibiology-microscopy-course.html
- An online course covering all aspects of light microscopy in a series of video lectures
- https://www.ibiology.org/ibioeducation/taking-courses/ibiology-microscopy-short-course.html
- A short course covering the basics
- Excellent microscopy reference for beginners and experts by M. W. Davidson and the Florida State University
http://www.gensat.org/index.html
- 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
- 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 is a communication network between European scientists working in the field of light microscopy and the manufacturers. BIU is a member of ELMI
http://www.antibodies-online.com/
- An antibodies marketplace
- Novel Fluorescent Proteins etc. Part of Takara Bio
- CSHL Press provided web site where you can search for scientific supplies
- Primary antibodies for signal transduction molecules
- Photoactivable fluorescent proteins etc.
- A plotting tool for different protein properties
http://www.thermofisher.com/fi/en/home.html
- Previously lifetechnologies.com
- Labeled secondary antibodies etc.
- Sells CoralHue fluorescent proteins, also photochromic ones that are turned on or off on demand by exposure to different wavelenghts of light
http://www.sigmaaldrich.com/life-science/functional-genomics-and-rnai.html
- 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
- Antibodies as well as other immunohistochemistry /immunofluorescence products
- 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
- Free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images
- CellProfiler is a free open source software designed to quantitatively measure phenotypes from thousands of images automatically
http://icy.bioimageanalysis.org/
- Icy provides the software resources to visualize, annotate and quantify bioimaging data
http://www.imagemagick.org/script/index.php
- ImageMagick is a software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats
- KEGG is a 2-D visualization tool for metabolic pathways
http://code.enthought.com/projects/mayavi/
- Scientific data visualizer
- An open source software for image acquisition. ImageJ compatible user interface. Matlab programs can be utilized in Micro-Manager. (Windows, Mac, Linux
- Medical Image Processing, Analysis, and Visualization; NIH Java application that enables quantitative analysis and visualization of PET, MRI, CT, and microscopy images
http://www.openmicroscopy.org/
- OME is an open source software project to develop a database-driven system for the quantitative analysis of biological images
http://vcell.org/run-vcell-software
- Virtual Cell software from the National Resource for Cell Analysis and Modeling allows simulation of e.g. FRAP data and membrane diffusion
http://www.indiana.edu/~voxx/index.html
- Voxel-based real-time 3D image processing and rendering of multi-channel 3D and 4D data. (Windows, Mac OS X, Linux)
Imagej
- NIH program for image processing and analysis. (Windows, Mac OS 9, Mac OS X, Linux)
- https://imagej.nih.gov/ij/list.html
- Discussion list for ImageJ users and developers
- https://list.nih.gov/cgi-bin/wa.exe?A0=IMAGEJ
- Also list archives
- Fiji is an image processing package. It can be described as a "batteries-included" distribution of ImageJ (and ImageJ2)
- http://www.cs.cmu.edu/~kangli/code/Image_Stabilizer.html
- ImageJ plugin that corrects x-y movement of images in time-lapse image stacks
http://bigwww.epfl.ch/thevenaz/turboreg/
- An ImageJ plugin for the automatic alignment of a source image or a stack to a target image
- ImageJ plugin for volume rendering by Michael D. Abramoff
- Imaris multidimensional image data rendering, visualization, and analysis software
http://www.leica-microsystems.com/products/microscope-software/details/product/leica-las-x-ls/
- Leica LAS X software. Lite version available for Windows 7
https://www.nikoninstruments.com/en_EU/Products/Software
- Nikon imaging software. NIS-Elements Viewer available for Windows and OS X
- Huygens deconvolution software, also FluVR volume rendering software
https://www.zeiss.com/microscopy/int/products/microscope-software/zen-lite.html
- Zeiss ZEN Lite imaging software for Windows
https://www.btk.fi/cell-imaging/
- Turku Centre for Biotechnology
http://www.hi.helsinki.fi/amu/
- Electron, confocal and DIC microscopy. At Haartman institute (HFIC, BCIC)
- Helsinki Functional Imaging Center coordinates the imaging activities in the Helsinki area