Useful links
A plotting tool for different protein properties
Microscopy and Imaging (commercial reference sites)
Microscopy and Imaging (non-commercial reference sites)
Microscopy and imaging networks
Fluorophores and other molecular/cell biology products
Tutorials
- Optical Microscopy Primer
- Nikon MicroscopyU: Introduction to Confocal Microscopy
- Leica Science Lab: Fluorescent Dyes
- Leica Science Lab: Fluorescence Recovery after Photobleaching (FRAP) and its Offspring
- iBioEducation
- Confocal Microscopy tutorial, Advanced Microscopy unit, Haartman Institute
- Basics of Standard Deviation and Standard Error of Mean
- Colocalization basics
- About the Resolution
- Peter Evennett - Abbe's Diffraction Experiments
- The Illuminated Plant Cell
- Adding scale bars to images using ImageJ
- Bitplane learning center
- Cleaning objectives
- Removing oil or water from objectives
Fluorescent Spectra
- Fluorescence SpectraViewer (ThermoFischer)
- SearchLight (Semrock)
- Spectra Database at University of Arizona
- Omega Curvomatic
- Chroma Spectra Viewer
- Evrogen Spectra Viewer
- Filter Assistant (Zeiss)
- Novus Spectra Viewer
- http://www.nightsea.com/sfa-sharing/fluorescence-spectra-viewers/
A plotting tool for different protein properties
Software
- Leica LAS X Core Offline
- ZEN lite
- Bitplane Imaris suite
- Bitplane downloads (FileConverter, Scene Viewer, Xtension bundles)
- AutoQuant X3
- Image-Pro Video Tutorials
- Scientific Imaging and Analysis - Photoshop for science
- Fiji
- BioImageXD
- 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
Microscopy and Imaging (commercial reference sites)
- 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
- 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)
Microscopy and Imaging (non-commercial reference sites)
- 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.
Microscopy and imaging networks
- 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.
Fluorophores and other molecular/cell biology products
- http://www.antibodies-online.com/
- An antibodies marketplace
- https://www.takarabio.com/
- Previous Clonetech. Novel Fluorescent Proteins etc.
- 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/
- 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, labeled secondary antibodies etc.
Free imaging software
- 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
- 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
- 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)
- 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.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.cs.cmu.edu/~kangli/code/Image_Stabilizer.html
- ImageJ plugin that corrects x-y movement of images in time-lapse image stacks
- 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://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)
Commercial imaging 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
Other imaging facilities
- 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