Automation and Real-Time Image Processing Documentation Version 1
This document provides guidance for understanding and implementing the set of workflows included in this collection. It outlines best practices and recommendations to ensure successful setup and execution of automated and real-time image processing pipelines.
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Automation and Real-Time Image Processing documentation.pdf
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Created: 24th Jun 2025 at 10:33
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Version 1 (earliest) Created 24th Jun 2025 at 10:33 by Daniel Marchan
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Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.
Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.
Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.
Adapting to Tilted Samples
To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle ...
Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.
Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.
Adapting to Tilted Samples
To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:
- Motion Correction Filters: Max ...
Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.
Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using CryoSPARC.
Adapting to Tilted Samples
To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:
- Motion Correction Filters: ...
Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using CryoSPARC.
Image processing from movies to micrographs, including CTF estimation and quality filters for image curation.
Adapting to Tilted Samples
To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:
-
Motion Correction Filters: Max per-frame shift = 30; Global drift = 120.
-
CTF Consensus Filters: Adapted to 6.5 Å and 8.5 Å resolution cutoffs.
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**Defocus ...
Image processing pipeline from movies to micrographs, including CTF estimation and quality filters for image curation.
A collection of image processing templates designed to support data collection and automated processing for Single Particle Analysis (SPA) in cryo-electron microscopy. The workflows range from simple pipelines—including movie alignment, CTF estimation, and quality assessment—to fully automated 2D and 3D processing. Please select the workflow that best suits your needs.
