Links

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

• 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
  advanced open-source tool for image processing and analysis, lots of additional plugins available (cross platform)

McMaster Biophotonics Facility - Downloads 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
         o LSM Toolbox
           plug-in for ImageJ especially for *.lsm files

   * 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)

Mailing Listserver

   * CONFOCAL@LISTSERV.BUFFALO.EDU
     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