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

49 Tutorials

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

7 Slides

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

2 Video Recordings

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

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GitHub Activity

github Issues Reported

23 Merged Pull Requests

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

• Add FIESTA as funder in several tutorials
  imaging
• Add more details to Euro-BioImaging as contributor
  template-and-tools
• Add subtopics to imaging
  imaging
  fair
• Add tags to imaging tutorials
  imaging
  fair
• Include OSCARS-FIESTA as organisation
  template-and-tools
  imaging

Reviewed 105 PRs

We love our community reviewing each other's work!

• Pycytominer training
  imaging
• 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

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