Links

Revision as of 17:10, 25 June 2008

Confocal 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

• Jim Pawley Course Material
  pre-course reading chapters foo Jim Pawley's "3D Microscopy of Living Cells" course

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

Spectral Data

Invitrogen Spectra Viewer link

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

• BIO-RAD Microsciences fluorochrome database
  fluorochrome spectra database, search function, Java based

• 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

• Arizona web widget spectra viewer Another pretty good spectra viewer.

Free Software

Image Processing and Analysis

ImageJ: colocalization analysis with automated threshold

• ImageJ
  advanced open-source tool for image processing and analysis, lots of additional plugins available (cross platform)
  • McMaster Biophotonics Facility
    useful MBF ImageJ plug-in Bundle (continuation of WCIF bundle); also available: ImageJ Manual
  • LOCI Bio-Formats Library
    plug-in for ImageJ, imports popular microscopy file formats, including those from confocal systems
  • Biomedical Imaging Group of EPFL
    Plugins for ImageJ (Spot Tracker, MosaicJ, Advanced Depth of Focus...)
  • ImageJ @ Wikipedia
    further informations

• Improvision Volocity LE
  easy-to-use image viewer for various microscopy file formats, including confocal ones
  (Windows, Mac OS-X)

• 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 only)

• 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)

Image Acquisition

µManager: main panel link

• µManager
  open source software package for imaging and control of automated microscopes
  (Windows, Mac OS, Linux)

Mailing Listserver

• 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