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[Discuss-gnuradio] GNU Radio and Magnetic Resonance Force Microscopy (MR

From: Jonathan Jacky
Subject: [Discuss-gnuradio] GNU Radio and Magnetic Resonance Force Microscopy (MRFM)
Date: Fri, 28 Jan 2005 09:02:58 -0800 (PST)

I joined this list recently so I thought I should describe my project.

I'm looking into using GNU Radio for signal processing in Magnetic
Resonance Force Microscopy (MRFM).  MRFM has some similarities with
atomic force microscopy (AFM) and scanning tunneling microscopy (STM)
but MRFM can form a 3D image of the sample below the surface (not just
on the surface like AFM and STM).  MRFM uses a tiny cantilever with a
permanent magnet attached.  Its raw data are cantilever deflections
caused by the magnetic forces exerted by electron or nuclear spins in
the sample.  From this raw data, the positions of the spins in the
sample can be inferred.  We hope eventually to obtain atomic-scale
resolution 3D images of proteins and other interesting structures.

The particular application I am considering is cantilever control.  We
detect the position of the cantilever by interferometry --- our
interferometer plays the role that the receiving antenna plays in most
GNU Radio applications. We control the position of the cantilever by
driving a current through a control coil that exerts a magnetic force on the
permanent magnet at the cantilever tip --- our control coil is
analogous to the transmitting antenna in radio.

In our current MRFM device the signals of interest are at audio
frequencies; in future devices they may be at radio frequencies.
Since we provide closed loop control we require short latency between
input and output (fifty microseconds or possibly much less, depending
on the design).

Our present audio frequency controller uses a SHARC DSP board in a PC
(the PC itself doesn't do any of the signal processing --- it's just
used for programming the SHARC).  Our prototype RF controller is a VME
bus computer with multiple G4 processors and special purpose DSP
chips for mixing down on input/up on output (the control codes process
the mixed-down signals).

Our RF controller now runs a monolithic signal processing program.  I
had already started work on a more flexible signal processing
framework when I ran across GNU Radio --- which had already
anticipated much of what we planned to do.  We're also intrigued by
the USRP hardware.

I've only recently gotten GNU Radio (mostly) working on our favorite
platform, Mac OS X.  Haven't made any firm decisions yet.  One
alternative might be to dispense with all the special VME stuff and
just use the USRP.  Maybe we could do the entire control signal path
in the FPGAs on the board, only using the USB to load the FPGA program
and/or retune the filters.  Or we might mix down/up on the USRP and
control the mixed-down signals on the Mac.  We might even stick with
the VME stuff, run GNU Radio there, and use the onboard down/up mixers
as sources and sinks.  Our selection among these alternatives
(including whether to use GNU Radio at all) will depend on
performance (especially latency), correctness, robustness and
stability, and ease of programming.

Gosh, this got long.  I haven't got a question this time, just thought
I'd let you all know what I was up to.  Here is our group's web page:


There's a nice description of MRFM basics in this press release from
another lab.


Jon Jacky, University of Washington

PS - "we" includes John Sidles, Joe Garbini, Tom Kriewall, and several students and others who have moved on.

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