Confocal and Specialized Microscopy

The Confocal and Specialized Microscopy Shared Resource (CSMSR) provides advanced microscope systems for high-resolution, multidimensional optical imaging of living and fixed cells and tissues, including intravital 2-photon imaging, super-resolution microscopy, and laser capture microdissection. Ph.D.-level staff support all stages of an imaging project including experimental design, training on instrument use, and image acquisition as well as data analysis, interpretation, and presentation.  

Our technologies provide better resolution, speed, and versatility than typical lab microscopes.  

Our expert support helps you achieve results that are optimized, efficient, and reproducible.  

Technologies & Services Offered

  • Wide-field fluorescence and histology

    • Digital deconvolution  

  • Laser capture, UV micro-irradiation

  • Confocal imaging

    • Three 1-photon scanning confocal microscopes

    • Two 2-photon systems with resonant scanners

    • Spinning-disk confocal microscope

    • Intravital (live-animal) 2-photon imaging

  • Super-resolution imaging

    • Total internal reflection fluorescence (TIRF)

    • Structured illumination microscopy (SIM)

    • Stochastic optical reconstruction microscopy (STORM)

  • Long-term, high-content plate imaging

  • Plate reading

  • Image analysis and processing

    • Automated quantitative analysis

    • 3D rendering and animation

  • Imaging service  

Application Examples

  • Live cell, tissue, and animal imaging  
  • Large-area imaging  
  • Cleared tissue imaging  
  • Photobleaching (FRAP, FLIP, DNA DSB generation)  
  • Scratch-wound assays (including automated scratch generation)  
  • Brainbow, Confetti imaging  
  • Laser capture for DNA, RNA, or protein analysis  
  • Image analysis  
    • Count, morphology, intensity  
    • Colocalization, translocation  
    • Cell and particle tracking  
  • Time-lapse imaging 
  • Förster Resonance Energy Transfer (FRET) 

Location

Lasker Biomedical Research Building
3960 Broadway (Entrance on 166th St.)

3rd Floor, Room 320
Tel: (212) 342-3604

Contact for consultation or training: Confocal_HICCC@cumc.columbia.edu


User Policies and Fees

New users, or returning users with new experiments: Please contact us for a free consultation to discuss your experimental needs, choice of instruments, and sample preparation.  

You may choose to be assisted at the microscope by a staff member (Assisted Use), or request Training for independent microscope use.  

Assisted use and training are available from 9:30 a.m. to 5:00 p.m., Monday through Friday. 

We are now happy to provide a drop-off Imaging Service, for which you can provide samples for imaging by CSMSR staff. Please check with our staff to find out if this service is appropriate for your imaging applications. 

Training

  • Only trained and certified independent users may reserve and use equipment.  
  • All training must be performed by staff. 
  • Please request appointments for imaging service or training at least 7 days in advance. 
  • Certified independent users may use the microscopes at any time. 

Reservations

  • Reservations must be made at least 24 hours in advance, and no more than 7 days in advance. 
  • There is a 1-hour minimum reservation time for most instruments. There is a maximum reservation time of 4 hours per day and 8 hours per week during peak hours (9 am - 5 pm, Mon.-Fri.). There is no maximum reservation time outside peak hours. 
  • Reservations cancelled less than 24 hours in advance will be charged unless someone else can use the time (please contact users scheduled before and after you). There is NO CHARGE for cancellation at any time due to illness or quarantine. 

Safety

  • The core operates at BSL-1; all samples potentially containing pathogenic agents must be properly fixed. 
  • Follow current Columbia and Shared Resource guidelines for COVID safety. 

If your experiment requires an exception to any policy, please discuss it with the Technical Director. 

Hourly Rates

Initial consultation

  • No charge

Assisted use, training, or service

  • Cancer Center Members: $99.30 
  • Non-Cancer Center Members: $132.40 
  • External users: $211.84 

Peak hours are Monday through Friday, 9:00 a.m. – 5:00 p.m. 

Unassisted use, peak hours

  • Cancer Center Members: $54.45 
  • Non-Cancer Center Members: $72.60 
  • External users: $116.16 

Peak hours are Monday through Friday, 9:00 a.m. – 5:00 p.m. 

Independent use, off-peak hours

  • Cancer Center Members: $45.38 
  • Non-Cancer Center Members: $60.50 
  • External users: $96.80 

Image processing/analysis service, training, or programming

  • Cancer Center Members: $45.00 
  • Non-Cancer Center Members: $60.00 
  • External users: $122.40 

Image analysis workstation, unassisted

  • Cancer Center Members: $12.38 
  • Non-Cancer Center Members: $16.50 
  • External users: $26.40 

Technical support 

  • Included in user fee 

Online Reservations

The CSMSR uses the iLab Core Management System for service requests, equipment scheduling, and billing. 

Microscopes and Supporting Equipment 

Scanning Confocal (Nikon A1)

  • Nikon Ti Eclipse inverted microscope with motorized XY Stage and hardware autofocus 
  • Lasers: 405, 488, 561, 638 nm 
  • 4 PMT detectors for fluorescence 
  • Transmitted PMT detector 
  • Software: NIS-Elements 

Resonant Scanning 1- and 2-Photon Confocal (Nikon A1RMP)

  • Nikon Ti Eclipse inverted microscope with motorized XY Stage and hardware autofocus 
  • Lasers: 405, 488, 561, 638 nm visible; pulsed IR laser 680 -1040 nm (Coherent Chameleon II)  
  • Resonant scanner and piezoelectric focus for fast imaging 
  • Spectral detector for unmixing of overlapping fluorophores or autofluorescence 
  • 2 PMT and 2 GaAsP descanned detectors for fluorescence 
  • Transmitted PMT detector 
  • Tokai Hit stage-top incubator and objective heater for live imaging 
  • Targeted photobleaching, FRAP, FRET and FLIP capability 
  • 2-photon microscopy with 3 non-descanned detectors for deep (up to 1mm) or long-term imaging  
  • 25x/1.10 coverslip-corrected water-immersion IR lens 
  • Software: NIS-Elements 

Super-Resolution Structured Illumination/ Scanning Confocal (Nikon N-SIM/A1) 

  • Nikon Ti Eclipse inverted microscope with motorized XY Stage and hardware autofocus 
  • High-sensitivity confocal imaging: 
    • Lasers: 405, 488, 561, 638 nm  
    • 2 GaAsP detectors for fluorescence 
    • Spectral detector 
    • Transmitted PMT detector 
  • Structured illumination (SIM) super-resolution: 
    • Double the resolution of the conventional confocal microscope (lateral ~58-110nm; axial ~200-250nm) 
    • 3D Axial Range: up to 20μm 
    • Lasers: 405, 488, 561 nm  
  • Software: NIS-Elements 

Super-Resolution Localization Microscopy / Spinning-Disk Confocal / TIRF (Nikon N-STORM/Yokogawa CSU-X1)

  • Nikon Ti Eclipse inverted microscope with motorized XY Stage and hardware autofocus 
  • Lasers: 405, 488, 561, 640 nm 
  • Tokai Hit stage-top incubator and objective heater 
  • Piezo Z focus for fast Z stack acquisition 
  • Spinning-disk confocal (Yokogawa CSU-X1): 
    • Fast imaging of living or fixed samples 
    • Lower photodamage than scanning confocal imaging 
    • Cameras: sCMOS (Andor Zyla 4.2) or EMCCD (Photometrics Evolve) 
  • Stochastic optical reconstruction super-resolution (STORM):  
    • Allows imaging fixed samples with a lateral resolution of ~20-30nm and an axial resolution of ~50-60nm 
    • 3D resolution with depth of ~ 1 µm using astigmatic lens 
  • Total Internal Reflection Fluorescence (TIRF): 
    • Image events at the cell surface (~100nm) with superior signal-to-noise ratio. 
  • Software: NIS-Elements 

Laser Capture Microdissection / Histology / Fluorescence (Zeiss MicroBeam IV)

  • Zeiss AxioObserver.Z1 inverted microscope with motorized XY Stage and hardware autofocus 
  • Wide-field fluorescence imaging: 
    • Fast switching LEDs for multicolor imaging 
    • Orca ER cooled CCD camera 
  • Laser Capture Microdissection (LCM) and Microirradiation: 
    • Non-contact laser catapulting for capturing live cells or material from frozen or paraffin-embedded tissue sections
    • Captured material can be used for isolation of DNA, RNA, or protein, or for cell/tissue culture applications 
    • 355-nm laser can also be used for: 
      • Creating localized double-strand breaks in DNA 
      • Ablating cells or subcellular structures
      • Photobleaching or photoactivation 
  • Color histology imaging with Axiocam ICc  
  • Fluorescence excitation: Mercury halide lamp with fluorescence filters; LEDs at 390, 455, 470, 505, and 590 nm 
  • Software: Zen Blue; PALM Robo 

Intravital Multiphoton / Scanning Confocal (Leica TCS SP8)

  • Leica DM6000 upright microscope with motorized XY stage 
  • Resonant scanner and Galvo Z focus for fast imaging  
  • 6 PMTs and hybrid (HyD) detectors with photon counting for sensitivity and quantitative analysis 
  • Spectral detection for unmixing of overlapping fluorophores or autofluorescence 
  • Transmitted PMT 
  • Pecon stage-top incubator for live cells 
  • Warming pad and anesthesia apparatus for intravital mouse imaging 
  • Targeted photobleaching, FRAP, FRET and FLIP capability 
  • 2-photon microscopy with non-descanned detectors for deep or long-term imaging 
  • Lasers: 458, 488, 514, 561, 640 nm visible; pulsed IR laser (700-900 nm) (Spectra-Physics MaiTai) 
  • Software: Leica LASX 

 Multi-Mode Plate Reader / Imager (BioTek Cytation/BioStack) 

  • Plate reader for UV-Vis absorbance, fluorescence and luminescence detection 
  • Robotic microplate stacker 
  • Brightfield, phase, color brightfield, and fluorescence imaging of microplates, slides, and 35-mm dishes 

Live-Cell Plate Imager / Incubator (BioTek Cytation/BioSpa)

  • Long-term imaging of up to 8 plates over periods of hours, days, or weeks 
  • Brightfield, phase, color brightfield, and fluorescence imaging of microplates, slides, and 35-mm dishes 
  • Robotic transfer of plates from incubator to temperature/CO2-controlled imaging platform 
  • Autoscratch device for automatic generation of scratch wounds in cell monolayers in 24- or 96-well plates 

Accessories

  • Lab bench with dissecting microscope, analytical balance, minifuge for 1.5 mL tubes, vortexer, water bath, and hotplate are available for basic sample preparation.  
  • Cell culture room with laminar flow hood, cell culture incubator, water bath, and 4° refrigerator  
  • Stagetop incubators for temperature, humidity, and CO2 control during experiments.  
  • Microfluidics and perfusion equipment 
    • Syringe pump  
    • Peristaltic pump 
    • CellAsic ONIX microfluidic system for mammalian cells, yeast, or bacteria on specialized plates 
  • Animal procedure area with isoflurane anesthesia machine, oxygen, warming pad

Image Analysis and Presentation

A Windows workstation with 256 GB RAM is available for image processing, analysis, and rendering. We provide consultation and training on analysis software. We also develop custom analysis workflows and scripts. Software includes: 

  • Imaris 9.9 
  • MATLAB 
  • Volocity Restoration (deconvolution), Visualization and Quantitation 
  • NIS Elements 
  • ImageJ/Fiji 
  • Cell Profiler 

Contacts

Acknowledgement and Co-authorship 

We expect that the Confocal and Specialized Microscopy Shared Resource and its funding will be acknowledged in all publications that use our instruments, software, and/or expertise. This helps ensure our continued operation and acquisition of new instruments. 

In addition, we welcome opportunities to provide significant intellectual and practical contributions that will lead to shared authorship. 

Sample text for acknowledgement: 
These studies used the Confocal and Specialized Microscopy Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University, funded in part through the NIH/NCI Cancer Center Support Grant P30CA013696.