Image-Analysis-Hub/Pasteur-BioImage-Analysis-Course-2025
May 2025 – May 2025
1 Month active
Languages Used
Jupyter NotebookMarkdownPython
Technical Skills
Bioimage AnalysisBioinformaticsCell SegmentationData AnalysisData VisualizationDocumentation
aliceblondel
PROFILE
Aliceblondel
Developed the RNA2seg notebook workflow for the Image-Analysis-Hub/Pasteur-BioImage-Analysis-Course-2025 repository, enabling scalable cell segmentation in large biological images with a focus on spatial transcriptomics. Leveraged Python scripting and Jupyter Notebooks to implement a five-step segmentation process, incorporating data analysis, visualization, and parameter tuning for reproducibility and teaching applications. Addressed a key bug by correcting placeholder path and alignment issues, ensuring accurate data handling and improved visualization. Enhanced documentation and technical writing supported user onboarding and workflow clarity. The work demonstrated depth in bioimage analysis, bioinformatics, and Zarr data handling, emphasizing reliability, performance, and maintainability throughout development.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
6Total
Bugs
1
Commits
6
Features
2
Lines of code
1,767
Activity Months1
Your Network
16 peopleWork History
May 2025
6 Commits • 2 Features
May 1, 2025Summary for 2025-05 (Image-Analysis-Hub/Pasteur-BioImage-Analysis-Course-2025): Delivered a robust RNA2seg notebook workflow enabling scalable cell segmentation in large biological images with spatial transcriptomics focus, with improvements to reliability, documentation, and performance metrics. Implemented core notebook development and usage workflow, fixed a placeholder path and alignment issue, and enhanced documentation and parameter tuning to support reproducibility and teaching use-cases. Major bug fix addressed placeholder path and text alignment to ensure correct data paths and improved visualization.
6 Commits • 2 Features
May 1, 2025Summary for 2025-05 (Image-Analysis-Hub/Pasteur-BioImage-Analysis-Course-2025): Delivered a robust RNA2seg notebook workflow enabling scalable cell segmentation in large biological images with spatial transcriptomics focus, with improvements to reliability, documentation, and performance metrics. Implemented core notebook development and usage workflow, fixed a placeholder path and alignment issue, and enhanced documentation and parameter tuning to support reproducibility and teaching use-cases. Major bug fix addressed placeholder path and text alignment to ensure correct data paths and improved visualization.
May 2025
Activity
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Quality Metrics
Correctness86.6%
Maintainability86.6%
Architecture80.0%
Performance73.4%
AI Usage20.0%
Skills & Technologies
Programming Languages
Jupyter NotebookMarkdownPython
Technical Skills
Bioimage AnalysisBioinformaticsCell SegmentationData AnalysisData VisualizationDocumentationJupyter NotebooksMachine LearningPython ScriptingSpatial TranscriptomicsTechnical WritingZarr Data Handling
Repositories Contributed To
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