Cell & Developmental Biology

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.

Carl Zeiss Microscopy Online Campus: A collaboration between Zeiss and Molecular Expressions

iBiology Microscopy Course: Online video lectures in basic and advanced techniques by experts in cutting-edge microscopy

Reference Tools

Addgene Fluorescent Protein Guide: One-stop shopping for fluorescent proteins and biosensors

Leica Guide to STED sample preparation: A must-read for anyone planning to use the Core's STED super-resolution system

Office of Research Integrity online learning tool and guidelines for image processing and manipulation

ImageJ User's guide: An essential reference for all users of ImageJ or Fiji (see Free Software section below).

Imaris Learning Center: Video tutorials and application notes designed to help new users of Imaris(commercial image analysis software available in our Core).

Volocity online training: A series of video tutorials to help you get started with Volocity, another commercial software packags available for use in our Core.

Fluorescence Tutorials: From Life Technologies, 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.

Life Technologies Fluorescence Spectrum Viewer

SearchLight from Semrock (a manufacturer of optical filters)

Chroma Spectra Viewer (Chroma is another 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.

ZEN Lite 2011 : Free software from Zeiss to open .lsm and .zvi files. This is the successor tothe LSM Image Browser and AxioVision LE, with expanded functionality. Note: this software does not include any 3D rendering capability. Windows only.

LAS AF Lite: Free software from Leica to open images acquired on the Leica SP8 confocal or any microscope controlled by LAS AF. Scroll down the linked page to find the version appropriate to your operating system. Windows only.

FileZilla Client: Recommended for SFTP transfer of files from the SOM Microscopy Core Server to your personal computer. Runs on PC or Mac. Instructions for using the server can be downloaded here (PDF file). *IMPORTANT* Do not use the Sourceforge installer on the main FileZilla Client download page, especially if you are using Windows. Adware and potentially unwanted programs (PUPs) will be installed along with FileZilla unless you are vigilent during the installation process. If you end up at the page showing the Sourceforge installer, click the link saying "Show additional download options" and select the desired version.



Dept. of Cell & Developmental Biology
421 Curie Boulevard
Philadelphia, PA 19104-6058
Tel: (215) 573-9306
Fax: (215) 898-9871