Measuring diffusion from time resolved EPR Imaging experiments

This Matlab App can be used to quantitatively monitor diffusion of EPR active guest molecules using time resolved EPR Imaging. It is provided in conjunction with the following publication, which contains step by step instruction on the usage:

Spitzbarth, M., Lemke, T., Drescher, M. In Situ Monitoring of Diffusion of Guest Molecules in Porous Media Using Electron Paramagnetic Resonance Imaging. J. Vis. Exp. (115), e54335, doi:10.3791/54335 (2016).

You can view the full video here.

Download: EPR Imaging Diffusion.mlappinstall

To install the app, make sure that easyspin is installed. Then double click on the downloaded file EPR Imaging Diffusion.mlappinstall. The app then appears in the Matlab program in the Apps tab.

EPR image reconstruction using SIRT

The software consists of the command line utility called reconstruct or it can be incorporated into your own software projects by calling the library functions directly from c++.

 

Source

Win32

Sample files

 

spectrum-0.1.0.zip

reconstruct.exe

samples.zip

GPG signature

spectrum-0.1.0.zip.asc

reconstruct.exe.asc

 

SHA1

05c34828f29b622b55f4f0ac68214a0e

4c6e7b922f4d0d59f5ddd34ef5c404ef

 

The GPG key can be found here (fingerprint: AE91 D535 FA3D AB31 241A  22E7 BE7C C8B0 C329 88C6).

For the windows binaries, you need to install the Visual C++ Redistributable Packages for Visual Studio 2013 (vcredist_x86.exe) available from the microsoft homepage.

Binaries for linux must be built from source.

If you publish results obtained by the use of this software, please cite the corresponding publication:

Martin Spitzbarth, Malte Drescher

Simultaneous iterative reconstruction technique software for spectral–spatial EPR imaging

J. Magn. Reson. 257, 79–88 (2015)

doi:10.1016/j.jmr.2015.06.001

Usage (2d spatial images)

  • Perform your EPR imaging experiment in the presence of a magnetic field gradient. The gradient strength must be constant, but the angle of  the gradient orientation must be changed between field sweeps.
  • Repeat the experiment in the absence of a magnetic field gradient.
  • Perform a deconvolution
  • Use the command line utility, for example:
reconstruct –-input your_deconvoluted_file.DSC –-output output.DSC –-steps 100 –-size 256
  • You will get files „output step 1.DSC“, „output step 2.DSC“, etc. Inspect these files, for example with an image stack in ImageJ to decide on the amount of steps for your final reconstructed image

Usage (1d spatial + 1d spectral)

  • Perform your EPR imaging experiment in the presence of a magnetic field gradient. The gradient orientation must be constant, and the strength oft he gradient must be changed between field sweeps.
  • Use the command line utility, for example:
reconstruct –-input your_experimental_data _file.DSC –-output output.DSC -–steps 100 –-size 256
  • You will get files „output step 1.DSC“, „output step 2.DSC“, etc. Inspect these files, for example with an image stack in ImageJ to decide on the amount of steps for your final reconstructed image.

Compilation from source and using the library in your own projects

Instructions on compilation can be found in the file Readme.txt in the source directory.

To see usage examples of the library, take a look at the test cases found in the tests subdirectory. Documentation can also be generated with doxygen from the doc target during compilation.