SEEK ID: https://workflowhub.eu/people/575
Location:
Spain
ORCID:
https://orcid.org/0000-0002-1442-3544
Joined: 28th Sep 2023
Expertise: Not specified
Tools: Not specified
Related items
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, MOLGENIS, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, OLCF-WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - 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Web page: Not specified
Scipion team located at the National Centre for Biotechnology (CNB, CSIC)
Space: Independent Teams
Public web page: https://scipion.i2pc.es/
Organisms: Not specified
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.
Creator: Daniel Marchan
Submitter: Daniel Marchan
Guidelines for using Scipion in the context of on-the-fly image processing at cryo-EM facilities. This document is divided into three main sections:
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On-the-fly processing: Monitoring data acquisition in real time.
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Processing workflows and templates: Building familiarity with creating and customizing workflows and templates in Scipion.
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Scipion with queue systems: Demonstrating Scipion’s behavior and integration with SLURM-based queueing systems.
Creator: Daniel Marchan
Submitter: Daniel Marchan
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.
Creator: Daniel Marchan
Submitter: Daniel Marchan
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.
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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.
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.
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 ...
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.
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.