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        • Spring3d
          • segmentrefine3d
          • segrefine3dinspect
          • segrefine3dgrid
          • seggridexplore
          • segmultirefine3d
          • segclassreconstruct
          • segrefine3dplot
          • segrefine3dcyclexplore
          • segclassmodel
        • Spring2d
          • segment
          • segmentexam
          • segmentclass
          • segmentalign2d
          • segclassexam
          • segclasslayer
          • seglayer2lattice
          • segmentplot
        • Springmicrograph
          • scansplit
          • micexam
          • michelixtrace
          • michelixtracegrid
          • micctfdetermine
          • scanrowcolcorr
          • scandotfit
          • scanlinefit

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  • Gallery
    • Spring3d
      • segmentrefine3d
      • segrefine3dinspect
      • segrefine3dgrid
      • seggridexplore
      • segmultirefine3d
      • segclassreconstruct
      • segrefine3dplot
      • segrefine3dcyclexplore
      • segclassmodel
    • Spring2d
      • segment
      • segmentexam
      • segmentclass
      • segmentalign2d
      • segclassexam
      • segclasslayer
      • seglayer2lattice
      • segmentplot
    • Springmicrograph
      • scansplit
      • micexam
      • michelixtrace
      • michelixtracegrid
      • micctfdetermine
      • scanrowcolcorr
      • scandotfit
      • scanlinefit
  • « About
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  • Gallery¶

    Spring3d¶

    Segmentrefine3d¶

    Program to iteratively refine 3D structure of helical specimens from segment stacks

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    Input: Image input stack refinement

    Output: Output volume name

    Segrefine3dinspect¶

    Program to interactively inspect 3D reconstructions from segmentrefine3d using slice viewer

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    Input: Volume reconstruction

    Output: Interactive screenshot

    Segrefine3dgrid¶

    Program to optimize segmentrefine3d reconstruction by varying refinement parameters systematically on a grid

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    Input: Image input stack refinement

    Output: Output volume name

    Seggridexplore¶

    Program to interactively explore grid searches according to different criteria

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    Input: Grid database

    Output: Subgrid merge option

    Segmultirefine3d¶

    Program to iteratively refine multiple 3D structures of helical specimens competitively from segment stacks

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    Input: Image input stack refinement

    Output: Output volume name

    Segclassreconstruct¶

    Program to compute 3D reconstruction from a single class average using a range of different helical symmetries

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    Input: Class average stack

    Output: Volume name

    Segrefine3dplot¶

    Program to plot refinement parameters from segmentrefine3d

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    Input: refinement.db file

    Output: Interactive screenshot

    Segrefine3dcyclexplore¶

    Program to interactively explore refinement cycle statistics

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    Input: refinement.db file

    Output: Interactive screenshot

    Segclassmodel¶

    Program to assign a series of 3D models to class averages

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    Input: Reference volumes

    Output: Class average stack

    Spring2d¶

    Segment¶

    Program to extract overlapping segments from micrographs

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    Input: Micrographs

    Output: Image output stack

    Segmentexam¶

    Program to examine all excised in-plane rotated segments and compute their collapsed (1D) and 2D power spectrum and width profile of helices

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    Input: Image input stack

    Output: Diagnostic plot

    Segmentclass¶

    Program to classify excised in-plane rotated segments using SPARX’s k-means clustering

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    Input: Image input stack

    Output: Class average stack

    Segmentalign2d¶

    Program to align segments from helical specimens with a restrained in-plane rotation of 0 or 180 +/- delta degrees

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    Input: Image input stack

    Output: Image output stack

    Segclassexam¶

    Program to examine helix classes to compute their collapsed (1D) and 2D power spectrum and width profile of helices

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    Input: Class average stack

    Output: Diagnostic plot

    Segclasslayer¶

    Program to extract amplitudes and phases from desired layer lines of class averages

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    Input: Class average stack

    Output: Interactive screenshot

    Seglayer2lattice¶

    Program to simulate helical diffraction pattern and plot helical lattice from a series of indexed layer lines or rise/rotation parameters

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    Input: Analyze power spectrum

    Output: Power spectrum input image

    Segmentplot¶

    Program to plot parameters from segmented helices

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    Input: spring.db file

    Output: Interactive screenshot

    Springmicrograph¶

    Scansplit¶

    Program to split large scan into individual micrographs. The location of individual micrographs is determined by a dummy micrograph reference.

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    Input: Micrographs

    Output: Output micrograph pattern

    Micexam¶

    Program to examine micrograph quality by computing a localized power spectrum using EMAN2’s e2scaneval.py and an averaged power spectrum from overlapping tiles using SPARX’ sx_welch_pw2.py

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    Input: Micrographs

    Output: Diagnostic plot pattern

    Michelixtrace¶

    Program to trace helices from micrographs

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    Input: Micrographs

    Output: Diagnostic plot pattern

    Michelixtracegrid¶

    Program to trace helices from micrographs

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    Input: Micrographs

    Output: Diagnostic plot pattern

    Micctfdetermine¶

    Program to determine CTF parameters from a set of micrographs using CTFFIND and CTFTILT (Mindell and Grigorieff JSB, 2003)

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    Input: Micrographs

    Output: Diagnostic plot pattern

    Scanrowcolcorr¶

    Program to evaluate the performance of scanner by correlating adjacent rows and lines with each other from a pure noise image.

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    Input: Micrograph

    Output: Diagnostic plot

    Scandotfit¶

    Program to evaluate performance of scanner by measuring dots spaced 2.5 mm apart.

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    Input: Micrograph

    Output: Diagnostic plot

    Scanlinefit¶

    Program to evaluate scanner performance of scanner by measuring deviation from 45 degree line to determine CCD curvature and pincushion parameter.

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    Input: Micrograph

    Output: Diagnostic plot

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    Source

    © Copyright 2010 - 2021, Carsten Sachse.
    Last updated on Mar 22, 2021.
    Created using Sphinx 3.5.3.