Beatriz Serrano-Solano

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

2 Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

• Topic: Image analysis using Deep Learning
• Topic: Imaging

48 Tutorials

• Single Cell / Analysis of plant scRNA-Seq Data with Scanpy ✍️ 🧐
• Single Cell / Generating a single cell matrix using Alevin 🧐
• Using Galaxy and Managing your Data / Submitting sequence data to ENA 🧐
• Using Galaxy and Managing your Data / Using dataset collections 🧐
• Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data 🧐
• Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) 🧐
• Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab 🧐
• Imaging / Using BioImage.IO models for image analysis in Galaxy 🧐
• Imaging / Content Tracking and Verification in Galaxy Workflows with ISCC-SUM 🧐
• Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME 🧐
• Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy 🧐
• Imaging / Nucleoli segmentation and feature extraction using CellProfiler ✍️ 🧐
• Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines 🧐
• Imaging / Voronoi segmentation 🧐
• Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy 🧐
• Imaging / Execute a BiaPy workflow in Galaxy 🧐
• Imaging / Training Custom YOLO Models for Segmentation of Bioimages 🧐
• Imaging / Tracking of mitochondria and capturing mitoflashes 🧐
• Imaging / Analyse HeLa fluorescence siRNA screen 🧐
• Imaging / Object tracking using CellProfiler ✍️ 🧐
• Imaging / Introduction to Image Analysis using Galaxy 🧐
• Imaging / Where to start with bioimage analysis in Galaxy ✍️ 🧐
• Imaging / Segmentation of Anatomical Structures in Medical 3-D Images 🧐
• Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools 🧐
• Microbiome / 16S Microbial analysis with Nanopore data 🧐
• Introduction to Galaxy Analyses / A short introduction to Galaxy 🧐
• Development in Galaxy / Generic plugins 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana ✍️ 🧐
• FAIR Data, Workflows, and Research / REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data 🧐
• FAIR Data, Workflows, and Research / FAIR Bioimage Metadata 🧐
• Foundations of Data Science / Python - Loops 🧐
• Foundations of Data Science / Python - Files & CSV 🧐
• Foundations of Data Science / Python - Basic Types & Type Conversion 🧐
• Foundations of Data Science / Python - Functions 🧐
• Foundations of Data Science / Python - Subprocess 🧐
• Foundations of Data Science / Python - Argparse 🧐
• Foundations of Data Science / Python - Lists & Strings & Dictionaries 🧐
• Foundations of Data Science / Python - Flow Control 🧐
• Foundations of Data Science / Python - Try & Except 🧐
• Foundations of Data Science / Python - Math 🧐
• Foundations of Data Science / Python - Introductory Graduation 🧐
• Foundations of Data Science / Python - Globbing 🧐
• Introduction to Galaxy Analyses / Breve introducción a Galaxy - en español 🧐

7 Slides

• Using Galaxy and Managing your Data / Submitting SARS-CoV-2 sequences to ENA 🧐
• Climate / Functionally Assembled Terrestrial Ecosystem Simulator (FATES) 🧐
• Imaging / Nucleoli Segmentation
  &
  Feature Extraction
  using CellProfiler ✍️ 🧐
• Introduction to Galaxy Analyses / A Short Introduction to Galaxy 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana 🧐
• Introduction to Galaxy Analyses / Una Breve Introducción a Galaxy 🧐

2 Video Recordings

• Visualisation / Visualisation with Circos 💬
• Galaxy Server administration / Connecting Galaxy to a compute cluster 💬

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GitHub Activity

github Issues Reported

21 Merged Pull Requests

See all of the github Pull Requests and github Commits by Beatriz Serrano-Solano.

• Add subtopics to imaging
  imaging
  fair
• Add tags to imaging tutorials
  imaging
  fair
• Include OSCARS-FIESTA as organisation
  template-and-tools
  imaging
• Add AI4Life to the list of funders
  template-and-tools
• Update my details

Reviewed 104 PRs

We love our community reviewing each other's work!

• Imaging: add an Earth Observation path to the CellProfiler object-tracking tutorial
  imaging
• Imaging: add an Earth Observation path to the BioImage.IO models tutorial
  imaging
• Add tutorial: Segmentation of Anatomical Structures in Medical 3-D Images
  imaging
  faqs
• Training Update: OMERO suite tutorial with new credential system
  imaging
• Add CYOA feature to split Voronoi segmentation tutorial by scientific field
  imaging

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