Available services include: 

We are not the only light microscopy core facility at Johns Hopkins University. We will try to keep the links below up to date - if you find a non-functional link, or would like us to add a link, please contact George McNamara,  with information.


JHU Light Microscopy Cores
JHU iLabs Organizer JHU / JHMI wide core resources

iLabs Organizer ... we  suggest you search for   confocal

MicFac East Baltimore - Physiology Bldg

lots of equipment and staff

MPI Core (Neurosci P30) East Baltimore - PCTB

multiphoton and confocal

Microscopy and Imaging Core Facility (MICF)

East Baltimore -

Robert H. and Clarice Smith Building

Wilmer Eye Institute 



ICE East Baltimore - Miller Research Bldg

Institute for Cellular Engineering




The department has a Nikon epifluorescence microscope equipped with a CCD camera for digital imaging. This unit is a core facility, available to departmental members at large. In addition, the department has an Olympus Fluoview 300, laser-scanning confocal microscope that is shared among several departmental laboratories that competed successfully for an NIH shared instrumentation grant. The confocal microscope is equipped for simultaneous electrophysiological and patch-clamp recording, and has custom lasers permitting CFP/YFP FRET imaging.


MRB Molecular Imaging Service Center and Cancer Functional Imaging Core (MRB - miller Research Bldg)      (iLab Organizer)

Multiphoton Intravital Microscope

  • The Olympus FV1000MPE multiphoton laser-scanning microscope offers bright, clear imaging deep within specimens. The microscope is equipped with a wide variety of regular and water immersion objectives for in vivo and ex vivo imaging (see table below). In addition, our facility also carries a special 20 X MicroProbe objective that allows high-resolution imaging in vivo. This MicroProbe objective has a unique design employing a characteristic long, narrow tip that is optimized for insertion into an animal’s body to allow observation of various fluorescence signatures. The tunable pulsed laser with a range of 690 nm to 1040 nm and 3 standard Photo Multiplier Tube (PMT) light detectors (2 have spectral discriminations) enables the detection of fluorescence markers such as most Alexa dyes, Fluorescent proteins, DAPI, Rhodamine, Calcein, Fluo-3, Fluo-4, Indo-1, FITC, Hoechst, and second harmonic signal generating and auto-fluorescing molecules such as collagen I and NADH. The specialized microscope software and motorized x-y stage allows for users to take z-stacks, time series, and tile images of true 12 bit acquisition with up to 4096 by 4096 pixels. Application: a>Imaging neural networks in the brain. b> Photoreceptors in the retina. c> Cancer cell and tissue structures in the various vital organs of small animals such as mice or rats. d> SHG Imaging for Collagen 1 fibers. Animals and specimens that are still radioactive at a low dose will be allowed on this microscope to integrate multiphoton microscopy into multimodal imaging studies using PET and SPECT.
Cell Imaging Core Facility The Sidney Kimmel Comprehensive Cancer Center   (iLab Organizer)

  • Nikon C1si True Spectral Imaging Confocal Laser Scanning Microscope System. One of the advantages of conventional Confocal microscopy is the ability to optically section tissue or cells therefore eliminating out-of-focus glare. The C1si also has the capability of acquiring 32 channels of fluorescent spectra over a 320 nm wide wavelength in a single pass using spectral imaging.
  • Nikon E-600 is an upright microscope with a Nikon DS-Fi2 camera connected. The E-600 scope uses Elements for fluorescent microscopy and for brightfield microscopy.
  • E-800 is an upright Microscope. This also has a CCD camera attached to it for imaging of fluorescent slides using Elements software.
  • Leica LMD 7000 Microscope. Used for laser capture microdissection.
  • Nikon SMZ 1500 fluorescent stereoscopic zoom microscope is suitable for quickly assessing the presence of fluorescent proteins, such as GFP in live cells. In addition, the low magnification capability permits photography of whole tissue mounts using Elements and Act-1 software.
  • TE-200 + CCD camera - Inverted Microscope. Also has CCD Camera attached for imaging of culture flasks/plates using Elements software.
  • Nikon TE2000E is an inverted microscope. 
  Homewood - IIC

​IIC Light Microscopy (20180501 list)

• Zeiss LSM 800 Confocal with AiryScan supper-resolution module, motorized stages and 405, 488, 561 and 633nm lasers  and Pecon incubator(acquired with funds from NIH SIG award #1S10OD020152-01A1, McCaffery PI)

• Lavision BioTECH Ultramicroscope II lightsheet microscope equipped with 405, 488, 561, 640, and 785nm lasers and okoLab incubator (acquired with funds from NIH SIG award #1S10OD020152-01A1, McCaffery PI)

• Two Zeiss LSM 700 confocals with Pecon cage incubators for live imaging. Lasers include 405, 488, 555, and 633 nm.

• Zeiss LSM 780 confocal microscope with Pecon cage incubator;

• Zeiss AxioObserver Yokogawa CSU-X1 spinning disk confocal equipped with dual Evolve EMCCDs, 405/488/561and 633nm lasers, FRAP module, and stage incubator for live imaging. (acquired in part with NIH S10 award #1S10OD010712-01A1, PI McCaffery)

• Zeiss LSM 510 Multiphoton and Confocal equipped with Confocor 3 Fluorescence Correlation Spectroscopy module an

• Zeiss AxioObserver Epifluorescence SIM microscope equipped with Apotome 2 and Hamamatsu Orca Flash 4.0 CMOS camera. (acquired in part with NIH S10 award #1S10OD010712-01A1, PI McCaffery)

• 3i Marianas Live Cell Imaging Workstation with In Vivo Scientific cage incubator equipped with dual Cascade II 512 EM cameras for simultaneous 2-channel acquistion and TIRF (acquired in part with NIH S10 award #1S10OD010712-01A1, PI McCaffery)

• Zeiss Axiovert 200 LM with In Vivo Scientific cage incubator equipped with excitation and emission filter wheels; and Cooke Sensicam camera; also equipped for microinjection and micromanipulation (acquired in part with funds from NIH SIG award #1S10RR019409-01, McCaffery PI)

• Zeiss Axiovert 100 LM equipped with a CoolSnap digital monochrome camera; and and I-Pentamax 512 digital camera (acquired in part with funds from NIH SIG award #1S10RR019409-01, McCaffery PI; and NIH R01GM060979-06, Wendland PI)

• Zeiss Axioplan II LM equipped with a Cooke Sensicam digital monochrome camera; and a Q-Imaging color camera (This system is excellent for polarized microscopy and color photomicrography.)

• Zeiss AxioZoom V16 Fluorescence Stereoscope equipped with Axiocam MRm camera.

Note: accessories not listed here.



Carnegie embryology Carnegie Institute for Science - Department of Embryology (next to JHU Homewood campus)
HI^2 BME & more

Hopkins Imaging Initiative (BME centric, radiology, image processing, some microscopy)

Welcome to the Hopkins Imaging Initiative (HI^2), a collaborative resource for all of the imaging research at Johns Hopkins University. HI^2 consists of Hopkins researchers who focus on image acquisition, analysis, and application. 

Some of our current goals:

Connect researchers who develop and utilize imaging technologies
Organize seminars to showcase faculty and student research
Provide advice for incoming students
Compile a database of imaging resources
Evaluate classes, media, and resources
Create an informational forum to initiate innovations in imaging 

This resource was primarily created by the students of the Johns Hopkins Training Program in Translational Imaging.
If you are interested in receiving more information about events involving the Hopkins Imaging Initiative, we invite you to Join the Initiative  


More cores (for various applications) and links

GCRC "web notes"  (links to monthly calendar)



Other Baltimore Area Academic Confocal Core's

(note: we and/or the sites may not keep up to date)




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