SUSAN Documentation

General Information

• Overview
  • Key features at a glance
  • Contributing
  • License
  • Acknowledgements
  • Logos and media
• CryoET Background
  • Phase contrast and the Contrast Transfer Function
  • The missing wedge
  • Subtomogram Averaging
  • SUSAN: Substack Analysis
  • Spectral weighting in the reconstruction
• Why SUSAN?
  • Native projection-domain design
  • Performance and scalability
  • Accuracy
  • Modularity and flexibility
  • Similar works
• Installing SUSAN
  • Quick install
  • Prerequisites
  • pip into an existing environment
  • conda environment with system build tools
  • Self-contained conda environment (CUDA 12)
  • HPC / SLURM clusters
  • Building from source (custom configurations and MATLAB)
• Basic Concepts
  • From specimen to structure
  • Key terms
  • Data organisation
  • Processing modules
  • The iterative refinement loop (MACE)
  • Typical workflow
  • Quick example
• Common operations/Usage Examples
• Tutorials
  • EMPIAR-10064

Python API

• susan
  • read()
  • susan.data
    • susan.data.Tomograms
      • Tomograms
    • susan.data.Reference
      • Reference
    • susan.data.Particles
      • Particles
    • susan.data.TiltRangeSelector
      • TiltRangeSelector
    • susan.data.Particles.Geom
      • PtclsGeom
    • susan.data.Particles.MRA
      • PtclsMRA
  • susan.modules
    • susan.modules.Aligner
      • Aligner
    • susan.modules.Averager
      • Averager
    • susan.modules.SubtomoRec
      • SubtomoRec
    • susan.modules.CropProjection
      • CropProjection
    • susan.modules.CtfEstimator
      • CtfEstimator
    • susan.modules.CtfRefiner
      • CtfRefiner
  • susan.project
    • susan.project.STA
      • STA
    • susan.project.SubtomogramGenerator
      • SubtomogramGenerator
    • susan.project.ProjectionExtractor
      • ProjectionExtractor
    • susan.project.SubtomoAvg
      • SubtomoAvg
    • susan.project.SubtomoAvgMonitor
      • SubtomoAvgMonitor
    • susan.project.SubtomoAvgSched
      • SubtomoAvgSched
    • susan.project.SubtomoAvgN2N
      • SubtomoAvgN2N
    • susan.project.SubtomoAvgBase
      • SubtomoAvgBase
    • susan.project.SubtomoAvgCore
      • SubtomoAvgCore
    • susan.project.Schedulers
      • Bandpass
      • Angular Search
      • Iteration Type
    • susan.project.diagnostics
      • bandpass_shell_sweep()
      • Inter-iteration deltas
      • Prior sigma estimates
  • susan.ml
    • susan.ml.VolumePairs
      • VolumePairs
    • susan.ml.Noise2Noise
      • Noise2Noise
    • susan.ml.Noise2NoiseTrainer
      • Noise2NoiseTrainer
  • susan.io
    • susan.io.em
      • read()
    • susan.io.mrc
      • read()
      • write()
      • get_info()
    • susan.io.tlt
      • read()
    • susan.io.xf
      • read()
  • susan.utils
    • susan.utils.datatypes
      • fsc_info
      • ssnr
      • bandpass
      • search_params
      • offset_params
      • refine_params
      • range_params
      • mpi_params
      • inversion_params
      • boost_lowfreq_params
    • susan.utils.functions
      • dose_from_fsc()
      • radial_average()
      • fsc_get()
      • fsc_analyse()
      • fsc_get_fpix()
      • ssnr_from_fsc()
      • bandpass()
      • apply_FOM()
      • spectral_weight_CFSC()
      • apply_spectral_weight()
      • phase_randomize()
      • fsc_sharpen()
      • fsc_sharpen_filter()
      • get_extension()
      • is_extension()
      • force_extension()
      • time_now()
      • create_sphere()
      • bin_vol()
      • bin_frame()
      • bin_frame_shape()
      • mask_diameter()
      • angular_step_from_fsc()
      • is_odd()
      • is_even()