Back to Central Microscopy Facility

CMF Equipment

The Central Microscopy Facility supply year round and summer investigators as well as courses with instrumentation, some owned by MBL and some on loan, so please read through this guide to familiarize yourself with the Facility. Feel free to contact the Facility personnel for more information. Some of the CMF rooms are on the MBL One Card access system. You will need to get CMF authorization for your card to work on those CMF doors.

Scheduling Time and Trainings:
We use an on-line system by Stratocore for scheduling time and for setting up training sessions on individual microscopy systems. See this page for instructions.

Contact Louis Kerr at Marine Biological Laboratory, Woods Hole, Ma, 02543, Phone:  (508) 289-7273, Email: lkerr@mbl.edu for more information.

Electron Microscopy

TEM JEOL JEM-200CX Microscope
Microscope Name:
TEM JEOL JEM-200CX
General Overview:
80-200KV TEM equipped with:

- Low magnification mode (+/- 60 degrees tilt and 300 degree rotation)
- Standard specimen cartridge and goniometer specimen cartridge
- AMT digital side mount and bottom mount cameras

Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Electron
Detector:
Camera
Location - Building and Room
Lillie 208
Contact person:
Louie Kerr
Hourly Rate for Use:
$35/hr
Microscope with computer and multiple monitors.
Microscope Name:
ThermoFisher Helios 5 Hydra PFIB-SEM with Cryo and EDS/EBSD
General Overview:
A dual-beam high-resolution scanning electron microscope with ion beam milling capability. It is equipped with multiple detectors and four different ions and can perform conventional cross-section FIB-SEM as well as spin-milling to collect larger fields of view (<115 microns) at up to 5 x 5 x 5 nm resolution. It is also equipped with cryo-imaging capabilities and EDS (Energy Dispersion Spectroscopy) and EBSD (Electron Backscatter Detection).
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Electron
Features:
- Plasma milling capabilities using Xenon, Argon, Nitrogen or Oxygen
- Gas injection system (GIS) for deposition
- ThermoFisher cryo stage with Leica transfer system and prep station
- Oxford Instruments AZtec EDS/EBSD microanalysis system
- ThermoFisher Auto Slice & View software for FIB-SEM acquisition
- ThermoFisher MAPS software for array tomography and tile-scanning
Accelerating Voltage:
- 0.5-30 kV accelerating voltage, 1.5pA-2.5uA current range
Temperature Control:
Yes (cryo only)
Location - Building and Room:
Lillie 207
Hourly Rate for Use (internal users):
$36.75/hr for SEM use; additional $24.15/hr for use of cryo, EDS/EBSD or $50/hr for FIB-SEM"

Light Microscopy

Leica Stellaris 8 STED
Microscope Name:
Leica Stellaris 8 STED
General Overview:
The Leica Stellaris is a laser-scanning confocal microscope equipped with a white light laser and tunable emission filters for maximum flexibility in excitation/emission wavelength selection. It has a environmental control chamber and features an optional z-galvo stage for rapid, smooth acquisition of 3D volumes. The Stellaris is also equipped with stimulated emission depletion (STED) super-resolution and fluorescence lifetime imaging (FLIM) capabilities.
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Confocal, STED, FLIM
Microscope Stand:
Inverted
Features:
- Leica Dmi8 microscope body with conventional and z-galvo motorized stages
- Cage incubator for environmental control
- 405 laser and white light laser for excitation wavelength selection
- tunable emission wavelength selection
- three STED lasers for super-resolution imaging
- Leica FALCON FLIM analysis software
Laser Wavelengths:
405, white light laser (450-770), STED (536, 635,770)
Excitation/Emission Filters:
Tunable
Detector:
HyD PMTs
Imaging lenses:
10x/0.4 dry,20x/0.75 dry, 40x/1.1 W, 86x/1.2 W, 100x/1.4 oil (others available)
Microscope Control software:
Leica LAS X
Temperature Control:
Yes
CO2 Control:
Yes
Humidity Control:
Yes
Light Tight:
Yes
Sample mounting requirements/constraints:
Conventional sample mounting
Location - Building and Room:
Lillie 209
Hourly Rate for Use (internal users):
$34.65/hr (after 6 hrs, $17.33/hr)
Zeiss LSM 780 microscope
Microscope Name:
Zeiss LSM 780
General Overview:
The Zeiss LSM 780 is a multi-purpose, visible light confocal laser scanning microscope. It is equipped with a 34 channel spectral array with laser lines at 405nm, 458nm, 488nm, 514nm, 561nm, 594nm and 633nm. The LSM 780 is configured on an inverted Observer Z1 microscope with a motorized stage along with a variety of objectives.
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Widefield, Confocal
Microscope Stand:
Inverted
Features:
Capability of spectral imaging/linear unmixing
Laser Wavelengths:
405 nm, 458 nm, 488 nm, 561 nm, 594 nm, 640 nm
Excitation/Emission Filters:
DAPI (Zeiss 49) ; GFP (Zeiss 38HE) ; DsRed (Zeiss 43HE)
Detector:
PMT
Imaging lenses:
5x ; 10x ; 20x ; 25xOil ; 100xOil (more lenses available)
Microscope Control software:
ZenBlack2.3
Temperature Control:
No
CO2 Control:
No
Humidity Control:
No
Light Tight:
No
Sample mounting requirements/constraints:
Conventional sample mounting
Additional details:
Location - Building and Room:
Lillie 212
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$33/hr (after 6hrs $16.50/hr)
Sutter MOM 2P System microscope
Microscope Name:
Sutter MOM 2P System
General Overview:
The Movable Objective Microscope (MOM) from Sutter is a two-photon microscope capable of imaging deep within living specimens when combined with an appropriate laser. It provides 3-dimensional objective movement and rotation allowing the specimen to remain horizontal and stationary.
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Confocal, Multi-photon
Microscope Stand:
adjustable position (upright or inverted or in-between)
Features:
Objective rotates about optical axis for imaging ; customizable open platform design
Laser Wavelengths:
Coherent Chameleon Ultra2 laser offers a tuning range from 680nm to 1080nm
Detector:
PMT
Imaging lenses:
20xW, 0.8NA ; other lenses available
Microscope Control software:
MScan3.0
Temperature Control:
No
CO2 Control:
No
Humidity Control:
No
Light Tight:
No
Sample mounting requirements/constraints:
Conventional sample mounting as well as custom solutions
Location - Building and Room:
Rowe 203
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$33/hr (after 6hrs $16.50/hr)
Zeiss Axio Observer Spinning Disc microscope
Microscope Name:
Zeiss Axio Observer Spinning Disc
General Overview:
The Zeiss Cell Observer Spinning Disk confocal system has a Photometrics Evolve 512×512 camera. It is configured on an inverted Observer Z1 microscope with a motorized stage and a complete incubator chamber system.
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Widefield, Confocal
Microscope Stand:
Inverted
Features:
Electrophysiology equipment and FRAP module ; Evolve 512 Delta EMCCD Camera
 
Laser Wavelengths:
488 nm, 561 nm, 635 nm
Excitation/Emission Filters:
DAPI (Zeiss 49) ; GFP (Zeiss 38HE) ; DsRed (Zeiss 43HE) ; BS C/G/DR
Detector:
Camera
Imaging lenses:
10x ; 20x ; 40xOil ; 40xW ; 100xOil ; 150xGly
Microscope Control software:
ZenBlack2
Temperature Control:
Yes
CO2 Control:
Yes
Humidity Control:
Yes
Light Tight:
No
Sample mounting requirements/constraints:
Conventional sample mounting
Additional details:
Location - Building and Room:
Loeb G63
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$29.40/hr (after 6hrs $14.70/hr)
Zeiss Lightsheet7 microscope
Microscope Name:
Zeiss Lightsheet7
General Overview:
The Zeiss Lightsheet 7 is a stand-alone SPIM (Selective Plane Illumination Microscope) capable of imaging large, living specimens at much greater speeds than more traditional confocal technology. The fully motorized sample chamber translates in X,Y and Z as well as 360° rotation, which allows optical sectioning from virtually any angle within the specimen. The chamber is equipped for live imaging with control over temperature and CO².
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Widefield, Lightsheet
Microscope Stand:
Sample get introduced vertically into the microscope chamber.
Features:
One microscope chamber is larger and especially designed for holding media used for sample tissue clearing ; Camera: PCO edge 4.2 sCMOS
Laser Wavelengths:
405 nm, 488 nm, 561 nm, 647 nm
Excitation/Emission Filters:
DAPI (Zeiss 49) ; GFP (Zeiss 38HE) ; DsRed (Zeiss 43HE) ; Cy5 (Zeiss 50)
Detector:
Camera
Imaging lenses:
Illumination: 5x Multi Immersion ; 10x Multi Immersion
Detection: 5x Multi Immersion ; 10x (Zeiss loan) ; 20x Multi Immersion
Microscope Control software:
ZenBlack
Temperature Control:
Yes
CO2 Control:
Yes
Humidity Control:
Yes
Light Tight:
Yes
Sample mounting requirements/constraints:
Microscope chamber is virtually built around your sample, with its holder designed to best support your experiment's purpose. Sample holder interface is open both to custom design and machining and 3D printing of your own sample holder.
How to list instrument for inclusion in papers, reports and grant proposals:
The ZEISS Lightsheet 7 was supported by the Howard Hughes Medical Institute.
Location - Building and Room:
Loeb G58
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$35/hr (after 6hrs $17.50/hr)
diSPIM microscope
Microscope Name:
diSPIM
General Overview:
This microscope offers low photo-toxicity and large specimen handling of dual inverted selective plane illumination microscopy (diSPIM) with the power and flexibility of a live-cell microscope system. This system is  suitable for imaging samples in aqueous media.
Commercial or Pre-commercial:
Pre-Commercial
Which Facility:
CMF, Imaging Innovation Initiative
Imaging Mode:
Optical
If Optical:
Lightsheet
Microscope Stand:
Custom designed for upright applications
Features:
Suitable for imaging large samples at high volumetric speed.
Laser Wavelengths
405 nm, 488 nm, 561 nm, 640 nm
Excitation/Emission Filters:
Quad band filter for 405/488/561/640 lasers.
Detector:
Camera
Imaging lenses:
14x, 0.4 NA Multi-immersion lenses; 23x, 0.7 NA Multi-immersion lenses
Microscope Control software:
MicroManager
Temperature Control:
Yes
CO2 Control:
No
Humidity Control:
No
Light Tight:
No
Sample mounting requirements/constraints:
 Conventional sample mounting
Location - Building and Room
Lillie 215
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$34.65/hr (after 6hrs $17.33/hr)
Zeiss Axio Imager.M2 Microscope
Microscope Name:
Zeiss Axio Imager.M2 - Manual Stage
General Overview:
Upright compound microscope set up for transmitted light techniques such as brightfield, phase and DIC, and also set up for epi-fluorescence with a X-Cite light source. It includes a a motorized Z-drive and Zeiss AxioCams (color and b/w).
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Widefield
Microscope Stand:
Upright
Features:
Epifluorescence ; Cameras: Zeiss AxioCam 503 (b/w) ; Zeiss AxioCam 305 (color)
Excitation/Emission Filters:
DAPI (Zeiss 49) ; AF488 (Zeiss 09) ; GFP (Zeiss 38HE) ; DsRed (Zeiss 43HE) ; Cy5 (Zeiss 50)
Detector:
Camera
Imaging lenses:
5x ; 10x ; 20x ; 63xOil ; 63xW ; 100xOil (more lenses available)
Microscope Control software:
ZenBlue3.1
Temperature Control:
No
CO2 Control:
No
Humidity Control:
No
Light Tight:
No
Sample mounting requirements/constraints:
Conventional sample mounting
Additional details:
Location - Building and Room:
Lillie 209
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$12.60/hr (after 6hrs $6.30/hr)
Observer M25 Microscope
Microscope Name:
Zeiss Axio Observer
General Overview:
The Zeiss Axio Observer is set up for transmitted light techniques such as brightfield, phase and DIC and epi-fluorescence with a Colibri LED illuminator and mercury halide lamp. It includes a motorized stage and a Zeiss AxioCam 702.  
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Widefield
Microscope Stand:
Inverted
Excitation/Emission Filters:
DAPI (Zeiss 49) ; GFP (Zeiss 38HE) ; DsRed (Zeiss 43HE)
Detector:
Camera
Imaging lenses:
2.5x ; 5x ; 10x ; 20x ; 40xOil ; 63xOil / Optovar 1x ; 1.6x
Microscope Control software:
ZenBlue3.4
Temperature Control:
Yes
CO2 Control:
Yes
Humidity Control:
Yes
Light Tight:
No
Sample mounting requirements/constraints:
Conventional sample mounting
Location - Building and Room:
Loeb G61
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$12.60/hr (after 6hrs $6.30/hr)
Zeiss Axio Zoom V16 Stereo Microscope
Microscope Name:
Zeiss Axio Zoom V16 Stereo Microscope
General Overview:
The Zeiss Axio Zoom V16 is a stereomicroscope that features a very high numerical aperture over a large field of view. This allows for bright fluorescence imaging of samples from 7x-112x magnification. It is a completely motorized stereomicroscope with automated Z and stage for 3D imaging as well as tiling that combine the highest magnification with the largest field of view.
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Widefield
Microscope Stand:
Upright
Features:
Range of magnification : 7x-112x
Equipped with Apotome2
Cameras: Zeiss AxioCam 712 (b/w) ; Zeiss AxioCam 512 (color)
 
Excitation/Emission Filters:
DAPI (Zeiss 49) ; GFP (Zeiss 38HE) ; DsRed (Zeiss 43HE), Cy5 (Zeiss50)
Detector:
Camera
Imaging lenses:
 
Microscope Control software:
ZenBlue3.4
Temperature Control:
No
CO2 Control:
No
Humidity Control:
No
Light Tight:
No
Sample mounting requirements/constraints:
Conventional sample mounting
Additional details:
Location - Building and Room
Lillie 210
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$12/hr (after 6hrs $6/hr)
Zeiss Axio Zoom V12 Stereo Microscope
Microscope Name:
Zeiss Axio Zoom V12 Stereo Microscope
General Overview:
The Discovery V12 is a stereo dissecting microscope set up for transmitted light techniques. It includes a VisiLED base.
Commercial or Pre-commercial:
Commercial
Which Facility:
CMF
Imaging Mode:
Optical
If Optical:
Widefield
Microscope Stand:
Upright
Features:
Equipped with a VisiLED base
Camera: Zeiss AxioCam MRc
Detector:
Camera
Microscope Control software:
AxioVision
Temperature Control:
No
CO2 Control:
No
Humidity Control:
No
Light Tight:
No
Sample mounting requirements/constraints:
Conventional sample mounting
Location - Building and Room
Lillie 210
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$12/hr (after 6hrs $6/hr)

Other Equipment

Formlabs and Makerbot 3D printer
Equipment Name:
3D printer Formlabs Form 3B+
General Overview:
Formlabs Form 3B+ is an industrial-quality desktop 3D printer that can produce functional, high-quality prototypes and end-use parts in record time. The Form 3+ offers reliable print quality and accuracy, easy setup and maintenance, and a wide range of high-performance materials.
Commercial or Re-commercial:
Commercial
Which Facility:
CMF
Features:
- Printing resolution 25-300μm (resin layer thickness);
- Build volume 14.5 × 14.5 × 18.5 cm (5.7 × 5.7 × 7.3 in);
- Printing resins available in: black, grey, clear, clear bio-compatible , flexible80A / more available by request;
- FormWash and FormCure for post-processing;
- Workstation with essential software;
Location - Building and Room:
Lillie 215
Contact person:
Louie Kerr, Carsten Wolff
Hourly Rate for Use:
$9/10ml used resin
Image Analysis lab
Equipment Name:
Image Analysis Laboratory
General Overview:
In 2020, the MBL launched its Image Analysis Laboratory to meet the computational needs for imaging and analysis. The Image Analysis Laboratory facilitates several high-end workstations and a GPU server to researchers and course students for data handling and analysis. Additionally, the Lab houses various commercial analysis software and custom designed software for image analysis.
Commercial or Re-commercial:
Commercial
Which Facility:
CMF; Imaging Innovation Initiative
Features:
Installed Software:
Imaris 9.5.1
Avia 11
Arivis
ZEN Blue 3.6
MATLAB
Fiji / ImageJ
Napari
Location - Building and Room:
Lillie 227
Contact person:
Louie Kerr, Carsten Wolff, Abhishek Kumar
Hourly Rate for Use:
N/A