Links

Revision as of 15:02, 4 June 2008

Confocal Infos and Introductions

• Molecular Expression Primer
  very comprehensive - provides information about various microscopy techniques, stainings and much more

• 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

• 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

Free Image Processing Software

ImageJ: colocalisation 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.<br(Windows only)

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