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National Center for Microscopy and Imaging Research (NCMIR) Center for Research in
Biological Systems
Basic Science Building, Room 1000
University of California, San Diego
9500 Gilman Drive
Dept. Code 0608
La Jolla, CA 92093-0608 USA
Voice: (858) 534-0276
Fax: (858) 534-7497

Resources

Higher Voltage Electron Microscopes

NCMIR's three intermediate high voltage electron microscopes (IVEMs) are specially equipped for electron tomography and provide access through remote instrumentation to powerful and unique high voltage electron microscopes.

IVEMs

JEM-3200EF IVEM (300 kV). Features custom optics for high-tilt conical illumination for optical sectioning, an energy filter, a piezo-enhanced, high-precision goniometer, three high-resolution digital detectors, and an updated hardware/software control system compatible with the Telescience Portal.
JEM-4000EX IVEM (400 kV).NCMIR has two of these instruments; a production instrument and a test/development resource. Both instruments are specially equipped for electron tomography. The production instrument features a high-contrast imaging mode and custom optics for high-tilt conical illumination for optical sectioning and is equipped for remote control via Telescience.

UHVEMs

Hitachi H-3000 UHVEM at Osaka University (3.0 MeV). NCMIR houses an exclusive remote kiosk for controlling the world's largest transmission electron microscope. This unique instrument is equipped for electron tomography and houses a Tietz 4K x 4K CCD detector. To support interactive Telemicroscopy, high-quality HDTV video from the instrument is streamed over the Internet. (Pictured third from top, right.)
JEM-ARM1300S "Morning Star" UHV-TEM at Korea Basic Science Institute (1.25 MeV). NCMIR has successfully integrated the first ultra-high voltage instrument to be installed in the 21st century for full remote control via Telescience. (Pictured fourth from top, right.)

TEMs

NCMIR houses three conventional transmission electron microscopes (TEMs), one equipped for cryoelectron tomography:

JEOL-1200 (120 kV) Transmission Electron Microscope
JEOL-1200 MKII (120 kV) Transmission Electron Microscope
JEOL-2000EX (200 kV) CryoElectron Microscope

Light Microscopes

Five specially equipped light microscopes are available at NCMIR:

Bio-Rad RTS2000 Real-Time Confocal/Multi-Photon Microscope.An inverted microscope equipped with high-precision XYZ stages under automated computer control for producing of very large field 3-D mosaics. Capable of collecting four-channel images at a speed of up to 120 frame per second. It also equipped with Total Internal Reflection Fluorescent (TIRF) Microscope for high sensitive imaging.
Custom Nikon RCM8000 Real-Time Confocal/Multi-Photon Microscope.An upright scope featuring high-speed multi-photon capabilities like the RTS.
Bio-Rad Radiance 2000 Confocal/2-Photon Microscope. Ultra-sensitive upright microscope able to acquire 16-bit data in 1024 x 1024 format using gallium arsenide phosphide PMTs.
Bio-Rad MRC1024 Confocal. Inverted microscope equipped with a high-precision XYZ stage under automated computer control that permits acquisition of very large field 3-D montages.
Olympus FluoView1000. Inverted microscope equipped with a high-precision closed loop XY stage under automated computer control for producing very large field 3-D mosaics. It also equipped with environment chamber for long time live cell imaging.
Olympus spinning disk confocal microscope. Upright microscope equipped with a high-precision closed loop XY stage and closed loop Z control with commercial mosaic acquisition software from MicroBrightField. It equipped with high resolution high sensitive CCD camera for high speed mosaic acquisition.
Olympus BX50WI.Specially equipped for cell filling using a Dage-MTI IR CCD camera and a Nikon NARISHIGE micromanipulation and microinjection system.

Other Equipment

Bal-Tec HPM 010 High Pressure Freezing Machine and Freeze Substitution Devices. High pressure freezing, when used in combination with freeze substitution, delivers the best specimen preparation method for preserving cell and tissue ultrastructure and, therefore, obtaining high resolution in situ data. With HPF, one can obtain specimens with good preservation deep into the tissue and is not restricted to surface layers or small isolated cells of limited surface-to-volume ratios. High pressures prevent the expansion of water, lower the freezing point, increase the freezing rate, and reduce the crystallization rate of ice. Because the freezing is not limited based on conduction of heat from the sample by a cold source, the overall effect results in obtaining a vitrified water state rather than a damaging crystalline ice environment over a much larger area than with propane jet freezing or plunge-impact freezing. This machine is capable of 2300-2600 bar of pressure with a duration of working pressure of at least 500 ms, and a cooling time from 0°C to -50°C in 10 ms.

Within the facility are the following:
- a freeze-substitution temperature controller
- a Reichert CS-Auto with UV head
- four Leica and Reichert ultramicrotomes, Reichert-Jung FC4D & FC4E cryokit accessories, and section counter for serial sectioning Zeiss Microm Cryostat
- 2 LKB glass knife breakers, several diamond knives, and a Leica VT1000E vibratome used for tissue sectioning

NCMIR's Bal-Tec freeze substitution unit and a fully programmable Leica AFS freeze substitution unit has a temperature range from -140°C to +65°C and is capable of low temperature embedding with a special UV spectral lamp in perfect GN2 atmosphere excluding humidity and oxygen.

Cell Filling Station Equipped for Intracellular Injection. A Dage-MTI IR CCD camera and a Nikon NARISHIGE micromanipulation and microinjection system are available.

Computing Facility

NCMIR established the Keck Center for Integrated Biology with support from an award from the Keck Foundation in 1999. The facility features two computational clusters, more than 12 TB of centralized storage, and networking resources connecting instruments, computational resources, and desktop computers to research networks and the commodity Internet at a total of 7 gbit/s. Most instruments in the facility are supported by a computer or group of computers. Data is collected on these computers and then transferred into centralized storage, from which the data is processed in the Keck facility on public workstations using resources from SGI, HP/Compaq, Dell, Sun and IBM. These resources have varying levels of capabilities with anywhere from one to four processors and from 4 GB to 32 GB of RAM. Larger computational challenges are processed on either the 32-node Pentium III cluster or the 21-node Opteron visualization cluster powering 20 displays on the BioWall. These local resources are complemented by a host of remote computational and storage resources brought to the users by the Telescience Portal infrastructure and dedicated remote resources online with the OptIPuter. The NSF sponsored OptIPuter is an IP-based computing platform in which dynamically controllable optical networks enable scientists to interactively visualize, analyze, and correlate their data from distributed sites.

An array of software packages for image processing and analysis are maintained by NCMIR. In addition to the in-house software (see Downloads page), a variety of commercial packages is available including the Analyze software package (from Dr. Richard A. Robb at the Mayo Foundation/Clinic), Bitplane Imaris, Neurolucida, and Amira. Several software packages are available for image deblurring and deconvolution, including AutoDeblur from AutoQuant.

NCMIR also provides the full complement of integrated software for handling the acquisition, processing, analysis, management, and display of image data. Refer to the Downloads page for further information.

NCMIR also serves as a BIRN rack endpoint and hosts the CCDB, an online resource for 3D light and electron microscopy.

Resources available include IVEMs, TEMs, light microscopes, and a computing facility.

JEM-3200F Microscope

JEM-3200EF IVEM (300 kV)

4000 Microscope

JEM-4000EX IVEM (400 kV)

Osaka Microscope

The world's largest microscope (3.0 MeV) at the Center for Ultra-High Voltage Electron Microscopy at Osaka University in Japan, remotely accessible from NCMIR over the Internet

Korean Microscope

Korea's 1.25 MeV UHVEM, one of the most technologically sophisticated in the world, remotely accessible through Telescience

RTS Microscope

Bio-Rad RTS2000 Real-Time Confocal/Multi-Photon Microscope

Radiance Confocal Microscope

Bio-Rad Radiance 2000 Confocal/2-Photon Microscope

Olympus spinning disk confocal microscope

Olympus spinning disk confocal microscope with commercial mosaic acquisition software

Olympus FluoView1000

Olympus FluoView1000 with stage under automated computer control for producing very large field 3-D mosaics


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