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

https://www.chroma.com/

• 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)

http://www.hamamatsu.com/

• CCD cameras, light sources, lasers, fibre optics etc.

https://ibidi.com/

• 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

http://www.omegafilters.com/

• 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)

https://www.thermofisher.com/fi/en/home/life-science/cell-analysis/cellular-imaging/high-content-screening.html

• 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

http://micro.magnet.fsu.edu/

• 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

http://www.eurobioimaging.eu/

• 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

http://www.embl.org/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

http://www.antibodies-online.com/

• An antibodies marketplace

http://www.clontech.com/

• Novel Fluorescent Proteins etc. Part of Takara Bio

http://www.biosupplynet.com/

• CSHL Press provided web site where you can search  for scientific supplies

https://www.cellsignal.com/

• Primary antibodies for signal transduction molecules

http://evrogen.com/

• Photoactivable fluorescent proteins etc.

http://www.fpvis.org/

• A plotting tool for different protein properties

http://www.thermofisher.com/fi/en/home.html

• Previously lifetechnologies.com

https://jireurope.com/

• Labeled secondary antibodies etc.

https://www.mblintl.com/

• 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

https://vectorlabs.com/

• Antibodies as well as other immunohistochemistry /immunofluorescence products

http://anduril.org/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

http://www.bioimagexd.net/

• Free open source software for analysis, processing and 3D rendering of multi dimensional microscopy images

http://cellprofiler.org/

• 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

http://www.genome.jp/kegg/

• KEGG is a 2-D visualization tool for metabolic pathways

http://code.enthought.com/projects/mayavi/

• Scientific data visualizer

https://micro-manager.org/

• An open source software for image acquisition. ImageJ compatible user interface. Matlab programs can be utilized in Micro-Manager. (Windows, Mac, Linux

https://mipav.cit.nih.gov/

• 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

https://imagej.nih.gov/ij/

• 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

http://fiji.sc/

• 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

http://bij.isi.uu.nl/vr.htm

• ImageJ plugin for volume rendering by Michael D. Abramoff

http://www.bitplane.com/

• 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

https://svi.nl/HomePage

• 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)

http://www.hfic.helsinki.fi/

• Helsinki Functional Imaging Center coordinates the imaging activities in the Helsinki area