Manual CEITEC CryoEM Facility Workflows Version 1
This document provides a detailed explanation of all the workflows, including their functionalities, problems they address, advantages, disadvantages, implementation requirements, and open points for future versions.
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Created: 4th Oct 2023 at 14:22
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Version 1 (earliest) Created 4th Oct 2023 at 14:22 by Daniel Marchan
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https://orcid.org/0000-0002-1442-3544
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Scipion team located at the National Centre for Biotechnology (CNB, CSIC)
Space: Independent Teams
Public web page: https://scipion.i2pc.es/
The ultimate-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by layer 0 and 1 workflows, this workflow aims to enhance the quality of both acquisition images and processing.
Quality control protocols
…
Combination of methods
- CTF consensus
- New methods to compare ctf estimations
- CTF xmipp criteria (richer parameters i.e. ice detection)
Advantages:
- Control of ...
The second-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by the layer 0 workflow, this workflow aims to enhance the quality of acquisition images using quality protocols.
Quality control protocols
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Movie max shift: automatic reject those movies whose frames move more than a given threshold.
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Tilt analysis: quality score based in the Power Spectrum Density (astigmatism and ...
The simplest workflow among a collection of workflows intended to solve tasks up to CTF estimation.
Basic processing pipeline
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Import movies
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Movie alignment (recommended 2 GPUs)
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CTF estimation
Monitor acquisition
- Monitor summary protocol:
- Monitor basic parameters (item counts, drift, resolution, astigmatism, defocus, etc.)
- Raise alarms (mail setting available)
- Provides information of the basic steps (html report)
A set of generic and automatic workflows designed to:
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Run on-the-fly and unattended.
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Maintain robust stability for a wide range of samples.
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Covers steps from movies to CTF estimation (for the moment).
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Monitor the acquisition process and provide user feedback.
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Comprise three proposed workflows, each with an additional layer of complexity.
