Leonid Kostrykin

Affiliations

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.

1 Editorial Role

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: Imaging

29 Tutorials

• FAIR Data, Workflows, and Research / FAIR Bioimage Metadata 🧐
• FAIR Data, Workflows, and Research / REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data 🧐
• Imaging / Nucleoli segmentation and feature extraction using CellProfiler 🧐
• Imaging / Segmentation of Anatomical Structures in Medical 3-D Images ✍️ 🧐
• Imaging / Analyse HeLa fluorescence siRNA screen ✍️ 🧐
• Imaging / End-to-End Tissue Microarray Image Analysis with Galaxy-ME 🧐
• Imaging / Voronoi segmentation ✍️ 🧐
• Imaging / Use Pycytominer in Galaxy for processing high dimensional image-based readouts 🧐
• Imaging / Introduction to Image Analysis using Galaxy ✍️ 🧐
• Imaging / Quantitative Analysis of Histological Staining Using Color Deconvolution 🧐
• Imaging / Execute a BiaPy workflow in Galaxy 🧐
• Imaging / Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines 🧐
• Imaging / Using BioImage.IO models for image analysis in Galaxy ✍️ 📝 🧐
• Imaging / Where to start with bioimage analysis in Galaxy ✍️ 🧐
• Imaging / Training Custom YOLO Models for Segmentation of Bioimages 🧐
• Imaging / Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy 🧐
• Imaging / Content Tracking and Verification in Galaxy Workflows with ISCC-SUM 🧐
• Imaging / Object tracking using CellProfiler 🧐
• Imaging / Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools 🧐
• Imaging / Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy 🧐
• Imaging / Tracking of mitochondria and capturing mitoflashes ✍️ 🧐

1 FAQ

• Changing the data type of multiple datasets or collections

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GitHub Activity

github Issues Reported

14 Merged Pull Requests

See all of the github Pull Requests and github Commits by Leonid Kostrykin.

• Update `Where to start with bioimage analysis in Galaxy`: Minor updates/fixes
  imaging
• Add tutorial: Segmentation of Anatomical Structures in Medical 3-D Images
  imaging
  faqs
• Add some tags for consistency
  imaging
• Update tutorial: Using BioImage.IO models for image analysis in Galaxy
  imaging
• Update tutorial: Using BioImage.IO models for image analysis in Galaxy
  imaging

Reviewed 39 PRs

We love our community reviewing each other's work!

• Pycytominer training: add contributors and editing
  template-and-tools
  imaging
• minor edits on clarity and grammar
  imaging
• Editing first visualization step of the tutorial now that we have the built-in TIFF preview
  imaging
• fix data library annotation
  imaging
• Feedback on tutorial stain quantification tutorial
  imaging

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