AFM-SPM/TopoStats
Jan 2025 – Sep 2025
4 Months active
Languages Used
PythonMarkdownBinary
Technical Skills
Data ProcessingImage AnalysisDeprecation HandlingImage ProcessingDocumentationBioinformatics
llwiggins
PROFILE
Llwiggins
Worked on the AFM-SPM/TopoStats repository, delivering features and fixes that enhanced data integrity, documentation, and research workflows. Developed and improved Jupyter and Marimo notebooks for grain statistics and DNA tracing, implementing dynamic data loading, visualization, and workflow guidance using Python and scientific computing libraries. Addressed data loss in grain processing by introducing a max-value merge, and maintained compatibility with evolving dependencies through targeted deprecation handling. Expanded and clarified documentation, including detailed tables and visuals, to improve onboarding and reduce support needs. Enhanced test coverage and code readability, contributing to reproducibility and maintainability across bioinformatics and image analysis pipelines.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
26Total
Bugs
3
Commits
26
Features
6
Lines of code
54,987
Activity Months4
Your Network
26 peopleSame Organization
@sheffield.ac.uk16
Shared Repositories
10
ahobbs7Member
Dan BradyMember
EvaMartinCMember
Max GamillMember
Neil ShephardMember
Neil ShephardMember
SylviaWhittleMember
TomCMember
TobiFirthMember
Work History
September 2025
17 Commits • 5 Features
Sep 1, 2025September 2025 (AFM-SPM/TopoStats): Delivered major notebook and workflow enhancements across Grainstats, TopoStats, and Tracestats, expanded test coverage, and improved documentation. Key outcomes include: enhanced Grainstats Notebook Suite with dynamic loading, visualization, and workflow guidance via grainstats.py (plus updates and final loading fixes); removal of an erroneous grainstats notebook to reduce confusion; introduction of TopoStats Advanced Analysis Notebook enabling DNA tracing and height profile extraction; Tracestats DNA Tracing Notebook with curvature visualization updates; expanded Test Resources and Test Suite for notebooks; and improved documentation with docstrings to support pre-commit and contributor onboarding. These efforts improve reproducibility, accelerate research workflows, and strengthen code quality and testing.
17 Commits • 5 Features
Sep 1, 2025September 2025 (AFM-SPM/TopoStats): Delivered major notebook and workflow enhancements across Grainstats, TopoStats, and Tracestats, expanded test coverage, and improved documentation. Key outcomes include: enhanced Grainstats Notebook Suite with dynamic loading, visualization, and workflow guidance via grainstats.py (plus updates and final loading fixes); removal of an erroneous grainstats notebook to reduce confusion; introduction of TopoStats Advanced Analysis Notebook enabling DNA tracing and height profile extraction; Tracestats DNA Tracing Notebook with curvature visualization updates; expanded Test Resources and Test Suite for notebooks; and improved documentation with docstrings to support pre-commit and contributor onboarding. These efforts improve reproducibility, accelerate research workflows, and strengthen code quality and testing.
September 2025
May 2025
7 Commits • 1 Features
May 1, 2025Concise monthly summary for 2025-05 for AFM-SPM/TopoStats focusing on GrainStats Documentation Enhancements. Key features delivered: GrainStats Documentation Enhancements across TopoStats with detailed all_statistics.csv column table, visuals clarifying class_number and subgrain_number, and a new image methods-09.png. Cross-referenced grain_finding docs, expanded vetting steps for multi-class masking, and improved readability/formatting in grainstats.md. Major bugs fixed: none reported; focus was on documentation quality. Overall impact: improved onboarding and developer efficiency, reduced support queries due to clearer data references, and increased maintainability. Technologies/skills demonstrated: documentation design, cross-referencing, image asset management, pre-commit formatting, and Git-based version control.
May 2025
7 Commits • 1 Features
May 1, 2025Concise monthly summary for 2025-05 for AFM-SPM/TopoStats focusing on GrainStats Documentation Enhancements. Key features delivered: GrainStats Documentation Enhancements across TopoStats with detailed all_statistics.csv column table, visuals clarifying class_number and subgrain_number, and a new image methods-09.png. Cross-referenced grain_finding docs, expanded vetting steps for multi-class masking, and improved readability/formatting in grainstats.md. Major bugs fixed: none reported; focus was on documentation quality. Overall impact: improved onboarding and developer efficiency, reduced support queries due to clearer data references, and increased maintainability. Technologies/skills demonstrated: documentation design, cross-referencing, image asset management, pre-commit formatting, and Git-based version control.
February 2025
1 Commits
Feb 1, 2025February 2025 - AFM-SPM/TopoStats: Stability and maintenance focus. No new features released. Fixed Pillow deprecation warning in unet_masking by updating image resizing to Image.Resampling.NEAREST, preserving nearest-neighbor behavior for channel masks and ensuring continued compatibility with Pillow 10+. This targeted change reduces runtime warnings and potential CI issues, and keeps the processing path stable for downstream users.
1 Commits
Feb 1, 2025February 2025 - AFM-SPM/TopoStats: Stability and maintenance focus. No new features released. Fixed Pillow deprecation warning in unet_masking by updating image resizing to Image.Resampling.NEAREST, preserving nearest-neighbor behavior for channel masks and ensuring continued compatibility with Pillow 10+. This targeted change reduces runtime warnings and potential CI issues, and keeps the processing path stable for downstream users.
February 2025
January 2025
1 Commits
Jan 1, 2025Monthly work summary focusing on key accomplishments for 2025-01. Implemented a data-merge change in AFM-SPM/TopoStats to preserve historical grain data by merging with a maximum value rather than overwriting. This ensures no data loss and enhances the accuracy of grain crop analysis.
January 2025
1 Commits
Jan 1, 2025Monthly work summary focusing on key accomplishments for 2025-01. Implemented a data-merge change in AFM-SPM/TopoStats to preserve historical grain data by merging with a maximum value rather than overwriting. This ensures no data loss and enhances the accuracy of grain crop analysis.
Activity
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Quality Metrics
Correctness93.0%
Maintainability92.4%
Architecture90.0%
Performance86.2%
AI Usage21.6%
Skills & Technologies
Programming Languages
BinaryMarkdownPython
Technical Skills
BioinformaticsCode FormattingCode ReadabilityData AnalysisData LoadingData ManagementData ProcessingData VisualizationDebuggingDeprecation HandlingDocumentationFile HandlingFile I/OImage AnalysisImage Processing
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