Reconstruction using INFR

Reconstruction using INFR

PyTom also supports a reconstruction algorithm called Iterative Nonuniform fast Fourier transform based Reconstruction method (INFR). For more details about this algorithm, please check: Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms, Y. Chen et al., JSB 2014.

The way to use it is simple:

pytom PathToPytom/reconstruction/reconstruct_INFR.py

It requires the following parameters:

• -d: The directory name, in which all the aligned and unweighted projections are stored. Note that the projections should be EM format and the tilt angle information must be specified in the headers!
• -i: Optional, the number of iterations to run. 10 by default.
• -o: Output filename.

Note that INFR requires a lot of memory. Currently it is limited to 1k x 1k projections on most computers (i.e., depending on the amount of memory you have). To create the aligned projections you can also use PyTom. Simply use the script for WBP reconstruction, but omit weighting and reconstruction (--weightingType 0):

pytom PathToPytom/bin/reconstructTomogram.py --tiltSeriesPath MyTiltSeriesDir \
        --tiltSeriesPrefix NameOfTiltSeriesFiles --firstIndex 1 --lastIndex MyLastIndex \
        --referenceIndex MyReferenceProjectionIndex --markerFile MyMarkerFile \
        --referenceMarkerIndex MyReferenceMarkerIndex --projectionTargets \
        MyFileNameOfAlignedProjections --projectionBinning MyBinning --weightingType 0