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Location of NCMIR within the University of California San Diego


The National Center for Microscopy and Imaging Research (NCMIR) is located on the University of California San Diego (UCSD) in California. I first visited NCMIR for two weeks in March 2010 and have used this page to type some brief notes, although the most important information is actually the two pages I've listed below:

Related/Child Pages:

Structure and Location

NCMIR itself is spread over three buildings, but the main part is in the Biomedical Sciences building - it's on the ground floor "room 1000", with the door on your immediate left as you enter the main automatic glass doors. A lot of NCMIR employees are located over at the "Calit2" building. ...

Map around campus


This is mostly for my own records, but here I've listed some of the microscopes and other resources at NCMIR. I'm sure I'll soon discover there's already a list somewhere.


  • Titan - bought 2009, 4kx4k, 300 keV TEM, TEM & STEM modes & cryo
  • JEOL 4000 #1 - 400 keV TEM - up to 1 micron thick, 4kx4k, tilt rotate holder, TEM & EM.
  • JEOL 4000 #2 - 400 keV TEM - 8kx8k! (custom built camera)
  • FEI Spirit - Anna primary user
  • JEOL 3200 - 300keV
  • JEOL 12,000 - 120 keV, immunolabelling - only one lef that shoots film
  • 3View Systems (specs) - can image multiple res (eg: 4kx4k or 4kx6k). 3x3 @ 8k (24kx24k pixels) > 1 hr per section. (cutting each section only 10 secs)
    • Resoluation... max ~2nm-5nm/pixel in XY and slices down to 50 nm thick.
    • GATAN camera - saves to propriety ".dm3" format - saves some good header info and then can convert to .tif stack or mrc for IMOD.
    • typically planes off 60mm at a time with diamond knife.... longer exposure heats specimen & means harder to cut. knife is 45 deg are trying 30 deg.
    • acquired an even faster 3view system, a Merlin recently.

NCMIR Software

Full list of software out of NCMIR is here.

  • TxBR - advanced system for reconstructing tomograms which (unlike IMOD) can input/take any number of tilt series/images from any angle and accounts for the curvilinear trajectories of electrons.
  • WebImage Browser (WIB) - brilliant web based tool to display large cell volumes in a similar manner to Google maps. Uses Flash and is under development by Steve Lamont. Is part of Cell Centered Database (CCCD) project.
  • Jinx - a segmentation program which uses NIF ontologies. Written in Java by Steve Lamont.

Calit2 Facilities

Some of the big "attractions" in Calit2:

  • NexCave - hat + ART tracker (+ 3D glasses) with 9 LCD screens
  • StarCAVE - hat + ART tracker (+ 3D glasses) 15 panels, each with two 2048x1536 projectors, completely complete surrounding you! (youtubue) (article)
  • Allioscopy - wall where 3D glasses not required.
  • Wall - giant wall with many lcd monitors.

NCMIR Facilities

At NCMIR we also have a couple of cool toys, both of which live in the NCMIR conference room:

  • NCMIR wall display - a 4x3 wall of monitors - just a baby compared to that at CalIt2
  • Stereo Pair Projector Screen - two projects projected overlapping onto the same screen, but with $6 polarized lens filters at perpendicular angles, this screen is designed to show full screen side-by-side 3D "stereo pair" movies (like the ones on youtube).

See Also