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decide which probe to use for certain EPR (electron paramagnetic resonance) oximetry experiments
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Probe.m
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rank_probes.m

README

This code can help you decide which probe to use for certain EPR (electron
paramagnetic resonance) oximetry experiments

The latest version of this code can be found at
https://github.com/jalan/probe_selection

- Instructions -----------------------------------------------------------------

The easiest way to use this code is probably to simply copy the example.m file
and modify it for your needs. It is heavily commented. You can see the figures
produced by this script at https://github.com/jalan/probe_selection/wiki

- Notes ------------------------------------------------------------------------

This code is based on our EPR experiment design papers, [1] and [2]; the same
assumptions that we rely on there apply here.

rank_probes assumes we are doing a single-scan acquisition, since this is the
current common practice.

The scores returned by rank_probes, and the values on the vertical axes of the
optional plots, are arbitrary in some sense: they depend on the values of
sigma_N and M that you supply.
 - If you DO know these values, great: the scores and plots will be realistic.
 - If you DON'T know these values, that's fine too: just provide some default
   values like sigma_N=1e18 and M=512; then the scores and the plots may not
   be realistic, but the probes will still be ranked correctly.

Please report any issues at https://github.com/jalan/probe_selection/issues, or
contact me directly if you prefer.

- See also ---------------------------------------------------------------------

https://github.com/jalan/dual-scan_acquisition, where the code and data needed
to produce the figures in [2] are available

- References -------------------------------------------------------------------

[1] "Optimization of magnetic field sweep and field modulation amplitude for
    continuous-wave EPR oximetry". Jason Palmer, Lee C Potter, Rizwan Ahmad.
    Journal of Magnetic Resonance, 2011.
    DOI: http://dx.doi.org/10.1016/j.jmr.2011.01.013
    PubMed: http://www.ncbi.nlm.nih.gov/pubmed/21334232
    PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086786

[2] "Dual-scan acquisition for accelerated continuous-wave EPR oximetry". Jason
    Palmer, Lee C Potter, David H Johnson, Jay L Zweier, Rizwan Ahmad. Journal
    of Magnetic Resonance, 2012.
    DOI: http://dx.doi.org/10.1016/j.jmr.2012.05.021
    PubMed: http://www.ncbi.nlm.nih.gov/pubmed/22820009
    PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3423522

- License ----------------------------------------------------------------------

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either (at your option) version 2 or version 3 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with
this program. If not, see <http://www.gnu.org/licenses/>.
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