Links

Revision as of 18:52, 28 November 2013

Microscopy - Infos and Introductions

Molecular Expressions Microscopy Primer: TIRF introduction link

• Molecular Expressions Microscopy Primer
  very comprehensive - provides information about various microscopy techniques, stainings and much more
  • Nikon MicroscopyU
    Nikons part of the MEM Primer
  • Olympus Microscopy Resource Center
    Olympus' part of the MEM Primer

• Carl Zeiss MicroImaging Campus
  tutorials about microscopy and digital imaing offered by Carl Zeiss company

• Nyquist Calculator
  calculate the - according to Harry Nyquist - perfect sampling for your setup

Sample mounting

• How to mount samples for high resolution microscopy?

• Which Coverslips to use for microscopy?

CCD cameras

• Photometrics learning zone
  nice collection about all kind of information concerning CCD cameras. Note: Photometrics offers a cost free, 2-day camera course, which is run every 3 months in the UK

Spectral & Optical Data

Invitrogen Spectra Viewer link

Online Spectra Viewer: full setup for acquisition of eGFP link

Fluorochrome Spectra

• Fluorescent Spectra Database by Carl Boswell, Urs Utzinger
  comprehensive database with sorted spectras and lasers, lamps and filter sets

• Invitrogen Fluorescence Spectra Viewer
  nice layout, no search function, Java based

• BD Biosciences Fluorescence Spectrum Viewer
  slightly different fluorochrome setup, i.e. some FACS dyes

• Online Spectra Viewer
  a lot of dyes, filters and lasers available, rather simple layout

• Fluorophores.org by TU Graz
  extensive database with spectras, lifetimes etc.

Filter Specifications

• AHF Analysentechnik Filtersystems
• Chroma Technology Corp Handbook of Optical Filters for Fluorescence Microscopy

Objective Data

• Zeiss objective database

• Leica objective database

• Olympus objective database

• Nikon objective list

Free Software

µManager: main panel link

Fiji/ImageJ: colocalization analysis with automated threshold

Image Acquisition

• µManager
  open source software package for imaging and control of automated microscopes, refer to the µManager Wiki for configurations etc.
  (Windows, Mac OS, Linux)

Image Processing and Analysis

• Fiji / ImageJ
  open-source software for microscopy-related tasks

• BioImageXD
  open-source image analysis software
  (Beta, cross platform)

• Zeiss ZEN LE
  new free Zeiss software for viewing and processing *.lsm images
  (Windows XP 32bit, Windows 7 32/64 bit)

• Zeiss LSM Image Browser
  traditional free Zeiss software, can open database (*.mdb) and images (*.lsm) including all comments and acquisition information
  (Windows only)

• Leica LAS AF Lite
  free Leica software, can open *.lif and *.lei files, acquisition information are accessible
  (Windows XP 32bit only)

• Olympus FV Viewer
  free Olympus software, can open *.oib and *.oif files from Fluoview Confocals
  (Windows XP 32bit only)

• Zeiss Axiovision LE
  free version of the Axiovision software, able to open *.lsm files as well, nice batch export
  (Windows only)

• IrfanView
  image viewer for common file formats like *.tif and *.jpg, provides simple processing and batch conversion, slide show etc.
  (Windows only)

Mailing Listserver

• The Microscopy Listserver
  mailing list for all topics related to microscopy, but with a focus on electron microscopy

• Confocal List Server
  Confocal Microscopy List, many subscribers and discussions, archive function

• ImageJ Mailing List
  lots of discussions, good if you are interested in using ImageJ more advanced

Companies

TILL Photonics: iMIC link

• Carl Zeiss MicroImaging GmbH
  LSM 710 and LSM 5 Live confocals, microscope frames and objectives

• Leica Microsystems
  SP5(-X) and SPE confocals, microscope frames and objectives

• Olympus Microscopy
  FV1000(MPE) confocal, microscope frames and objectives

• Nikon Instruments Europe B.V.
  A1(R) confocal, microscope frames and objectives

• Andor Technology
  Revolution, IQ software, system integration

• TILL Photonics
  iMIC, Polychrome

• Improvision
  Volocity

• Bitplane
  Imaris

• okolab
  stage incubators, cage incubators

• Ibidi
  single- and multi-well dishes with cover-slip bottom, stage incubator

• Molecular Devices
  MetaMorph, MetaVue

• Intelligent Imaging Innovations
  FLIM, Marianas, Everest, SlideBook software, system integration

• Sutter Instrument
  DG-4 lightsource, micromanipulators, accessories

• LaVision Biotec
  TriMScope 2-Photon, FLIM, software, accessories

• Photometrics
  cameras (CCD, EMCCD)

Our Friends and contacts

• Turku BioImaging (Finland)
• Biological imaging Development Center at UCSF
• IMP Vienna, BioOptics Facility
• McGill University Life Sciences Complex Imaging Facility
• The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) - Structural Cell Biology Group - core facility
• LMC Zürich
• Amsterdamm NL - Rob Wolthuis r.wolthuis at nki.nl