Data processing

Data storage and processing

Computing workflow

Under construction

Data processing computing resources on site

Under construction

Available reconstructions programs

Under construction

Available additional programs

Under construction

Remote acces to LINUX workstations

Remote acceess to the Linux worstations that enables data processing requires a Leiden University login account. once this is granted the details on how this can be done can be obtained from the Wiki. 

Most frequently used LINUX commands

Under construction

On-site network and Wiki

Under construction

Data pre-processing

Provides the user with optimized data ready for image processing.

  • A posteriori camera correction (as from Afanasyev et al., 2015, Scientific Reports)
  • Movie alignment (Using Drift Corr script from Li et al., 2013, Nat Methods)
  • Magnification correction (Grant and Grigorieff, 2015, JSB)
  • CTF estimation (CTFFIND 4, Rohou and Grigorieff, 2015, JSB)
  • Overall data quality assessment

Data processing and analysis 

Data processing will be done within a Scipion project environment.

  • Automatic particle picking
  • 2D classification
  • Initial model generation
  • 3D classification
  • 3D refinement

These are just to provide a general overview of the data, and does not provide a final structure as it it will be done as a first pass.