csbio

SPREAD

A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment

SPREAD integrates 2D image classification, 3D initial model generation, model selection, and 3D refinement.

SPREAD achieves a fully automatic workflow in which nearly no expert domain knowledge and interactive manual operation are involved.

Download SPREAD1.1

  • STEP1: NCEM clustering

    NCEM is a network-based clustering algorithm, which optimizes the 2D single-particle image network by recalculating the correlation between nodes using the network's local and global structure.

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  • STEP2: peak-finding based initial model generation

    Peak Finding algorithm chooses several peaks on the similarity distribution globally, and conducts weighting strategy on different orientation peaks for 3D reconstruction.

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  • STEP3: Initial model selection

    In initial model selection process, SPREAD conduct SRes resolution measurement algorithm for assessing the quality of initial models.

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  • STEP4: Model refinement

    SPREAD conducts a two-step refine strategy which combines peak-finding algorithm and network-based orientation search method for accurate model refinemnet.

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NEW FEATURES OF SPREAD1.1

SPREAD1.1 integrates a cryo-EM particle alignment toolkit(EMAF)

SPREAD1.1 integrates the EMAF toolkits for fast cryo-EM image alignment. EMAF is a power spectrum based fast alignment method.

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SPREAD1.1 conducts final resolution evaluation using SRes

SPREAD1.1 conducts SRes Resolution evaluation process after generating the final map. Providing a resolution value for your reference

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Automatic threshold determination for SRes algorithm

In the original version of SRes resolution measurement algorithm, the threshold parameters were assigned by users. But here in SPREAD1.1, we conduct parameter self-adaptive adjustment.

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