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Cell and Developmental Biology Microscopy Core (Penn)

Director: Stout, Andrea L., Ph.D.


The CDB Microscopy Core is the primary light microscopy facility for researchers at the Perelman School of Medicine at The University of Pennsylvania. We are also open to the entire University of Pennsylvania community as well as to CHOP, Wistar, and other local institutions. While our emphasis is on confocal and related technologies, our aim is to provide personalized assistance on all aspects of imaging, from tips on sample preparation to training on one of our microscopes to processing and analysis of image data.



    Member: Veklich, Yuri, Ph.D.
    Role: SEM Specialist, Cell and Developmental Biology Microscopy Core (Penn)

    Member: Zhao, Jasmine, M.Sc.
    Role: Confocal Specialist, Cell and Developmental Biology Microscopy Core (Penn)



  • Deltavision deconvolution microscope ( Deconvolution microscope )

    "Inverted microscope accommodates slides, 35-mm glass-bottomed dishes, or Lab-Tek II chambered coverglasses.

    Photometrics CoolSnap HQ high-resolution CCD camera

    Applied Precision x-y-z precision motorized stage for multi-point acquisition of image stacks

    Software-controlled filter wheels with DAPI, FITC, TRITC, Cy5, CFP, YFP filter sets; phase contrast & DIC available

    Environmental chamber surrounding entire microscope for temperature and CO2 control"

  • EVOS FL Auto cell imaging system ( Microscope )

    "With automated stage movement, filter and objective changes, focus, and exposure, the EVOS® FL Auto Cell Imaging System does the hard work for you. Simply set your parameters and let the EVOS® FL Auto take care of the rest. Perfect for area scanning, automated cell imaging, image stitching, and time-lapse imaging."

  • Leica STED 3X Super-resolution confocal microscope ( super-resolution microscope )

    • Two depletion lasers (592 and 660 nm) for super-resolution imaging of green and red dyes [Anatomy-Chemistry STED confocal]
    • Leica DMI 6000 inverted microscope
    • Pulsed white-light laser for tunable excitation from 470 to 670 nm
    • CW laser lines for conventional confocal imaging: 405, 458, 488, 514 nm
    • High-speed resonant scanner for live-cell imaging
    • 3 HyD and 2 PMT detectors
    • Tokai Hit stagetop incubator
    • Motorized xy stage
    • LAS X software for acquisition; Huygens Professional software for deconvolution

    Best suited for: ultra-high resolution (< 40 nm lateral, < 150 nm axial) imaging of fixed & live samples; fast confocal imaging of live specimens."

  • Leica TCS SP8 ( Confocal microscope )

    • DMI 6000 inverted microscope
    • LAS X software for acquisition
    • Excitation laser lines: 405, 488, 552, 638 nm
    • Three spectral detection channels: 2 PMTs and 1 HyD detector
    • Tokai-Hit stagetop incubation chamber
    • FRAP and FRET wizards
    • Motorized x-y stage for and tiling applications

    Best suited for: confocal imaging of fixed or live samples, including those requiring incubation; FRAP, photoactivation, or photoconversion in live cells or organisms; FRET"

  • Leica Widefield Deconvolution Microscope ( Deconvolution microscope )

    The Leica widefield deconvolution microscope features:

    • Leica DM6000 motorized upright microscope
    • Photometrics HQ2 high resolution monochrome cooled CCD camera
    • LAS AF software with AutoQuant deconvolution package
    • DAPI, FITC, Texas Red, and Cy5 filter cubes

  • Leica widefield microscope - Color camera ( Microscope )

    • Leica DMRBE upright microscope with halogen and mercury arc lamps
    • QImaging MicroPublisher 5.0 MP high resolution color CCD camera
    • iVision for Mac acquisition software
    • phase contrast, DIC, and polarized light transmitted light options
    • Filter sets for standard 3-color fluorescence imaging (DAPI, FITC, TRITC)

    Best suited for: Color imaging of fixed tissue stained with chromogenic dyes; polarized light microscopy; simple immunofluorescence imaging of fixed samples"

  • Spinning disk confocal #1 ( Spinning-disk confocal microscope )

    • Olympus IX71 inverted microscope
    • Hamamatsu ImagEM EMCCD camera
    • Excitation laser lines: 442, 488, 523, 561 nm (for CFP, GFP, YFP, and RFP)
    • Motorized xy stage for multi-point acquisition
    • Andor MicroPoint ablation laser (405 or 435 nm) for ablation or FRAP
    • LCI Chamlide stagetop incubation system for live mammalian cell imaging
    • MetaMorph acquisition software

    Best suited for: fast confocal imaging of sensitive, live samples; FRAP in live cells or organisms; FRET sensors (CFP-YFP or GFP-RFP)"

  • Spinning disk confocal #2 ( Spinning-disk confocal microscope )

    • Olympus IX81 inverted microscope
    • Excitation laser lines: 405, 488, 561 (for Hoechst, GFP, RFP)
    • Andor iXon3 EMCCD camera
    • Motorized x-y stage for multi-point acquisition or tile scanning
    • Roper iLas2 ablation laser (405 nm) for FRAP or photoactivation
    • Okolab stagetop incubation chamber
    • MetaMorph acquisition software

    Best suited for: fast confocal imaging of sensitive, live samples; FRAP, photoactivation, photoconversion in live cells or organisms"

  • Zeiss Axioplan widefield microscope ( Microscope )

    • Zeiss Axioplan upright microscope with Zeiss FluoArc mercury lamp
    • Zeiss AxioCam HRm high-resolution monochrome CCD camera
    AxioVision 4.5 software for acquisition and analysis
    • Filter sets for standard 4-color imaging (DAPI, FITC, TRITC, Cy5); also CFP and YFP filter set

    Best suited for: widefield epifluorescence imaging of fixed, fluorescent samples mounted on slides with coverslips"

  • Zeiss LSM 510 NLO/META ( Laser scanning confocal microscope )

    • Zeiss Axiovert 200M inverted microscope
    • Zeiss AIM software for acquisition
    • 2 PMT detectors plus 32-channel META detector for spectral detection
    • Tunable Ti-Sapphire laser for multi-photon excitation or second-harmonic generation (SHG)
    • Other laser lines: 458, 488, 514, 543, 633

    Best suited for: confocal imaging of fixed fluorescent samples or live samples at room temperature; second-harmonic generation imaging of collagen in unfixed or fixed tissue."

  • Zeiss LSM 710 Confocal Microscope ( Laser scanning confocal microscope )

    • Zeiss AxioObserver inverted microscope
    • ZEN 2012 software for acquisition
    • Excitation laser lines: 405, 458, 488, 514, 561, 594, 633 nm
    • Three spectral detection channels, including a 32-channel detector
    • Environmental chamber and motorized x-y stage for live imaging and tiling applications

    Best suited for: confocal imaging of fixed or live samples, including those requiring incubation; FRAP, photoactivation, or photoconversion in live cells or organisms; FRET; spectral characterization and linear unmixing of unorthodox dye combinations"

  • Zeiss Z1 Lightsheet ( Confocal microscope )

    "Imagine you had access to an imaging system that could deliver optical sections of large samples, with virtually no phototoxicity or bleaching and with high temporal resolution.

    That is exactly what Lightsheet Z.1 from ZEISS does. The unique Multiview light sheet fluorescence microscope allows you to record the development of large, living samples and gently image them to deliver exceptionally high information content.

    It is also fast: Lightsheet Z.1 is the tool you need to get optical sections at unprecedented speed. Acquire images of your whole sample volume at sub-cellular resolution – in a fraction of the time it takes using other techniques."


  • Imaging experimental design consultation service ( Support service )

    "Core staff members are available for consultation on design of imaging experiments."

  • Light microscopy assisted session service ( Support service )

    "You bring prepared samples and a Core staff member acquires the images for you. To book an assisted session, contact Andrea or Jasmine via email. Assisted sessions must take place during regular weekday hours (9:00am - 6:00pm, M-F). Recommended for users new to confocal or who need confocal images only occasionally."

  • Light microscopy unassisted session service ( Access service )

    "Users who have completed their hands-on training may book their own sessions through our online reservation system and work independently on any of our microscopes. Unassisted sessions can take place anytime, weekdays or weekends. Recommended for users who need to use our microscopes on a routine basis. For more information about our training program please read this page.

    Training: No charge for mandatory pre -training lecture. Hands-on training is $250 per person; this includes credit for the first three hours of unassisted use (unassisted sessions must take place within one month of hands-on training in order to qualify)."

  • Microscopy training service ( Training service )

    "No charge for mandatory pre -training lecture. Hands-on training is $250 per person; this includes credit for the first three hours of unassisted use (unassisted sessions must take place within one month of hands-on training in order to qualify)."

  • Scanning electron microscopy sample preparation service ( Material processing service )

    The service consists of three types of sample preparation:

    A: mount and Au/Pd sputter-coat, set of 1-6 samples
    B: fix, dehydrate, chemical drying, set of 1-6 samples
    C: critical point drying, set of 1-6 samples

  • Scanning electron microscopy service ( Analysis service )

    "Core staff member Yuri Veklich provides consultation, sample preparation, and imaging on the FEI Quanta 250 scanning electron microscope housed in the Electron Microscopy Resource Laboratory, suite B33 Anatomy-Chemistry Building. Contact Yuri directly at yuri AT mail.med.upenn.edu to learn more about SEM or to schedule an appointment."

    Sample Prep A: Fixation & Dehydration, set of 6 samples
    Sample Prep B: Mount & Au/Pd Sputter Coat, set of 6 samples


  • Axiovision LE ( Software )

    Available free of charge, AxioVision LE gives a first impression of the Zeiss microscope software AxioVision.

    "AxioVision LE reads and writes in the Carl Zeiss ZVI image format."

  • Fiji ( Software )

    "Fiji is an image processing package. It can be described as a distribution of ImageJ (and soon ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux."

  • GIMP ( Software )

    GIMP is an "open-source substitute for Adobe Photoshop and Illustrator."

  • Imaris ( Software )

  • iVision-Mac ( Software )

    "iVision‐Mac is image acquisition, processing, measurement, and analysis software. iVision‐Mac directly supports the acquisition of images and time-lapse series. Sophisticated imaging processes or even simple routines can be automated down to the push of a single button through the use of the intuitive scripting tool. There is no need to learn Visual Basic or other programming languages when you want to automate your imaging routines. Also, fully integrated extensions easily automate microscope control by driving motorized microscope hardware.

    Using spatially calibrated images with the automated measurement tools, scientists can quickly and easily perform dozens of image processing tasks. The resulting data can be saved in iVision‐Mac, or opened in a spreadsheet program such as Excel for further analysis. User definable plots and histograms are also included to present the data as desired. iVision‐Mac also includes densitometry measurements that can be used to plot an analysis such as mean intensity over time. iVision‐Mac supports the measurement of individual objects, regions of interest, and entire images. iVision‐Mac performs batch analysis of images and sequences using file lists and indexed files."

  • Leica LAS X ( Software )

  • MetaMorph ( Software )

    "MetaMorph Software provides all the tools needed to perform meaningful analysis of acquired images. Common tools for thresholding, filtering, and feature extraction are included as one would expect. However, MetaMorph Software provides other more sophisticated tools such as the integrated morphometry analysis (IMA) module. IMA allows objects to be measured and separated into user-definable classes, based on any combination of measured morphometric parameters, such as shape, size, or optical density. A point-and-click interface, linking images and spreadsheet results, makes it easy to choose representative objects for classification and measurement.

    MetaMorph Software also offers many user-friendly application modules for biology-specific analysis such as cell signaling, cell counting, and protein expression. Each application module features a dedicated dialog box with intuitive setting selections, improved segmentation through adaptation to local content, as well as both field and cell-by-cell data logging. After analysis is complete, users can interactively view tabular and image results side by side for their cellular imaging application."

  • OpenOffice ( Software )

  • SoftWoRx ( Software )

    "Deltavision's processing and deconvolution software, used primarily for post-acquisition processing of images acquired on the Deltavision Widefield imaging station"

  • Volocity ( Software )

    Volocity is a sophisiticated software for visualization, deconvolution, and quantitative analysis of 3- and 4-dimensional image data.

  • Zeiss AIM ( Software )

    Software that controls the Zeiss hardware and has powerful image processing capabilities, including time lapse, photobleaching, FRAP, FRET capability, and 3D visualization.

  • Zeiss Zen 2010 ( Software )

    Software for image acquisition.

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Last updated: 2016-06-29T17:09:02.435-04:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016