UPenn Cell & Developmental Biology

Microscopy Links

Educational Sites

Molecular Expressions Optical Microscopy Primer: From Florida State University, the first place to go for answers to all your microscopy questions.

Microscopy U: From Nikon and Molecular Expressions, another repository of microscopy information.

Fluorescence Tutorials: From Invitrogen, a series of tutorials on fluorescence-based techniques including flow cytometry.

Spectrum Viewers

These viewers are valuable tools for anyone preparing samples for fluorescence microscopy.

Invitrogen Fluorescence Spectrum Viewer

Spectrum viewer from the University of Arizona

"Curve-O-Matic" spectrum viewer from Omega Optical (a manufacturer of optical filters)

Free Software

ImageJ: ImageJ is free, open-source Java-based image analysis and processing software supported by the NIH. ImageJ can open many image file formats, including all those used by Core instruments. Runs on Mac OS, Windows, and Linux.

Fiji: ImageJ plus a large bundle of plugins, all packaged together in one easy-to-download application. Runs on Mac OS, Windows, and Linux. Very handy for new users who don't want to download individual plugins. Includes utilities for 3D viewing, video editing, measuring colocalization among others.

MBF ImageJ Bundle: This large collection of ImageJ plugins assembled by the McMaster Biophotonics Facility in Canada will greatly enhance the functionality of ImageJ.

LSM Image Browser and AxioVision LE: Free software from Zeiss to open, view, and export .lsm files acquired on the LSM 510 confocal or .zvi files acquired using AxioVision. Windows only.

LCS Lite: Free software from Leica to open, view, and export .lei files acquired on the Leica TCS SP2 confocal. Windows only.

ImageSurfer: From UNC-Chapel Hill, software for visualization and analysis of multi-channel 3D and 4D (time lapse) image data sets. Windows only.

BioImageXD: From the BioImageXD Project in Finland, open source software for analysis, processing and 3D rendering of multi dimensional image data sets. Runs on Mac OS X, Windows XP, and Linux.