Imaging Tools & Links

Software Downloads

• LAS AF Lite – A free (Lite) version of  Leica Application Suite Advanced Fluorescence software (LAS AF) can be downloaded from the Leica FTP site.  Go to ftp://ftp.llt.de/ , open the “softlib” folder, open the “LAS_AF_Lite” folder, and download the software.

This free version of LAS AF software has limited capabilities relative to the full version, but can be used to open and view .lif files, create maximum projections, add scalebars, take snapshots, and export images and movies.  Leica’s Lif format files can also be opened with Volocity software. 

• Volocity – http://cellularimaging.perkinelmer.com/downloads/detail.php?id=14

The newest versions of Volocity software are available here.  PVIC has a license server that can be used to enable the software.  If you would like to use Volocity and are not already registered to use the PVIC license server, please contact the core manager.

• ImageJ -  http://imagej.nih.gov/ij/  

Free ImageJ image analysis software download, plugins, and documentation can all be found here.

• Fiji (Fiji is just ImageJ)  –  http://fiji.sc/Downloads

As the name implies, this is ImageJ, but includes all plugins.

• CellProfiler – http://www.cellprofiler.org/

CellProfiler cell image analysis software and CellProfiler Analyst data exploration software are available for free download at this link.

Other Imaging Cores at the University of Pennsylvania & Wistar Institute

• CDB Microscopy Core at the Perelman School of Medicine – http://www.med.upenn.edu/cdbmicroscopycore/
• Wistar Imaging Facility – http://www.wistar.org/our-science/shared-facilities/imaging-facility
• Wistar Molecular Screening Facility – http://www.wistar.org/our-science/shared-facilities/molecular-screening-facility

The Molecular Screening Facility has High Content Imaging and Analysis capabilities.

• Electron Microscopy Resource Laboratory at the Perelman School of Medicine – https://somapps.med.upenn.edu/pbr/portal/morph/index.php
• Small Animal Imaging Facility at the Perelman School of Medicine – http://www.uphs.upenn.edu/radiology/research/labs/saif/
• Nano/Bio Interface Center – http://www.nanotech.upenn.edu/

     Anyone interested in doing Scanning Probe Microscopy (Atomic Force Microscopy) should contact the NBIC.

Online Tools & Useful Information

• Life Technologies Fluorescence SpectraViewer – http://www.lifetechnologies.com/us/en/home/life-science/cell-analysis/labeling-chemistry/fluorescence-spectraviewer.html

     The SpectraViewer shows excitation and emission curves for a wide variety of fluorophores, alone or in combination, and allows you to overlay wavelength information for light sources, excitation filters, and emission filters.

• Chroma Spectra Viewer – http://www.chroma.com/spectra-viewer
• Life Technologies Cell Staining Simulation Tool – http://www.lifetechnologies.com/us/en/home/support/research-tools/cell-staining-tool.html
• Fluorescent Protein Properties – http://nic.ucsf.edu/FPvisualization/ 
• ISS Lifetime Data of Selected Fluorophores – http://www.iss.com/resources/reference/data_tables/LifetimeDataFluorophores.html

Microscopy Education

• iBiology free microscopy course – https://www.ibiology.org/online-biology-courses/microscopy-series/

These are excellent lectures given by top scientists.

• Molecular Expressions Optical Microscopy Primer – http://micro.magnet.fsu.edu/primer/index.html

This site includes interactive tutorials and virtual microscopes that are very helpful for demonstrating various concepts related to different types of microscopy.

• Leica Science Lab –  http://www.leica-microsystems.com/science-lab/topics/ 
• Nikon Microscopy U –  http://www.microscopyu.com/ 
• Carl Zeiss Microscopy Online Campus – http://zeiss-campus.magnet.fsu.edu/index.html
• Olympus Microscopy Resource Center –  http://www.olympusmicro.com/