Imaging Tools & Links

Software Downloads

LAS X Office – A free offline version of the Leica LAS X microscope software for PC (sorry, no Mac version): https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/

This free version of LAS X will allow you to open and view .lif files acquired on our Leica microscopes, create maximum projections, add scalebars, take snapshots, and export images as .tif or .jpg files. Leica’s .lif format files can also be opened in FIJI, Volocity, and Imaris.

Volocity – This is a 3D image rendering and analysis software package. The Volocity software can be downloaded to your PC (sorry, again no Mac version) from here: https://www.volocity4d.com/download

To temporarily enable Volocity when needed, you can connect to the PVIC Volocity software license server. If you would like to use Volocity and are not already registered to use the PVIC license server, please contact the core manager.

Fiji (Fiji is just ImageJ): https://imagej.net/software/fiji/

This is ImageJ image analysis software, packaged together with the most common plugins.

Imaris viewer – This 3D/4D image viewer can be downloaded for free here: https://imaris.oxinst.com/imaris-viewer

The Imaris Viewer is a good tool for viewing image stacks in 3D but is not meant for image analysis. For 3D image analysis, the PVIC has a workstation with Imaris 3D image rendering and analysis software. Please contact the core manager if you wish to use Imaris at the PVIC.

CellProfiler – The Broad Institute’s CellProfiler cell image analysis software and CellProfiler Analyst data exploration software are available for free download at this link: http://www.cellprofiler.org/

QuPath – This image analysis software is especially useful for analysis of histological stains and can be downloaded for free here: https://qupath.github.io/

Other Imaging Cores at the University of Pennsylvania & Wistar Institute

• CDB Microscopy Core at the Perelman School of Medicine
• Wistar Imaging Facility
• Wistar Molecular Screening Facility – The Molecular Screening Facility has High Content Imaging and Analysis capabilities.
• Electron Microscopy Resource Laboratory at the Perelman School of Medicine 
• Small Animal Imaging Facility at the Perelman School of Medicine
• Nano/Bio Interface Center – Anyone interested in doing Scanning Probe Microscopy (Atomic Force Microscopy) should contact the NBIC.

Online Tools & Useful Information

• Life Technologies Fluorescence SpectraViewer – 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 
• Life Technologies Cell Staining Simulation Tool
• Fluorescent Protein Properties 
• ISS Lifetime Data of Selected Fluorophores 

Microscopy Education

• iBiology free microscopy course – These are excellent lectures given by top scientists.
• Molecular Expressions Optical Microscopy Primer – 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
• Nikon Microscopy U 
• Carl Zeiss Microscopy Online Campus 
• Olympus Microscopy Resource Center