ibs-lab/cedalion
Nov 2024 – Jun 2025
8 Months active
Languages Used
Jupyter NotebookPythonYAMLBibTeXMarkdownPytestSQLShell
Technical Skills
3D PlottingBug FixingCode FormattingCode RefactoringComputer VisionConfiguration
Eike Middell
PROFILE
Eike Middell
Eike contributed to the ibs-lab/cedalion repository by developing robust scientific data processing and modeling tools for neuroimaging and NIRS analysis. Over eight months, Eike engineered features such as out-of-core computation for large datasets, flexible GLM design matrix tooling, and cross-platform build automation. Using Python, NumPy, and Xarray, Eike improved data ingestion, error handling, and performance, while integrating advanced visualization and geometry registration workflows. The work included refactoring for maintainability, enhancing documentation, and expanding test coverage, resulting in a scalable, reliable codebase. Eike’s approach emphasized reproducibility, compatibility, and clear user guidance, demonstrating depth in scientific software engineering.
Overall Statistics
Feature vs Bugs
70%Features
Repository Contributions
98Total
Bugs
17
Commits
98
Features
39
Lines of code
14,201
Activity Months8
Your Network
10 people
Work History
June 2025
27 Commits • 10 Features
Jun 1, 2025June 2025 monthly summary for ibs-lab/cedalion: Focused on scalability, data-robustness, and release-readiness. Delivered out-of-core computation for fluence and sensitivity; integrated Schaefer parcellations for ICBM152/Colin27; exposed general affine register in TwoSurfaceHeadModel workflow; improved documentation and prepared release changelog; fixed TimeOffset handling for auxiliary channels to improve data robustness.
27 Commits • 10 Features
Jun 1, 2025June 2025 monthly summary for ibs-lab/cedalion: Focused on scalability, data-robustness, and release-readiness. Delivered out-of-core computation for fluence and sensitivity; integrated Schaefer parcellations for ICBM152/Colin27; exposed general affine register in TwoSurfaceHeadModel workflow; improved documentation and prepared release changelog; fixed TimeOffset handling for auxiliary channels to improve data robustness.
June 2025
May 2025
5 Commits • 3 Features
May 1, 2025May 2025 performance-focused monthly summary for ibs-lab/cedalion. Delivered robustness, reliability, and performance improvements across modeling, testing, and deployment. Key outcomes include (1) robust NaN handling in ar_irls_GLM fitting by masking non-finite values to prevent degraded iterations, (2) fixed bibliography syntax error in references.bib to ensure proper parsing and references integrity, (3) enhanced test infrastructure with a cross-platform temporary_filename context manager for Windows compatibility, (4) speedups in forward-model computations by applying NumPy matmul and re-packaging results as an Xarray DataArray for faster core calculations, and (5) reproducible deployments by pinning nirfaster to version 0.9.6 in the installation script.
May 2025
5 Commits • 3 Features
May 1, 2025May 2025 performance-focused monthly summary for ibs-lab/cedalion. Delivered robustness, reliability, and performance improvements across modeling, testing, and deployment. Key outcomes include (1) robust NaN handling in ar_irls_GLM fitting by masking non-finite values to prevent degraded iterations, (2) fixed bibliography syntax error in references.bib to ensure proper parsing and references integrity, (3) enhanced test infrastructure with a cross-platform temporary_filename context manager for Windows compatibility, (4) speedups in forward-model computations by applying NumPy matmul and re-packaging results as an Xarray DataArray for faster core calculations, and (5) reproducible deployments by pinning nirfaster to version 0.9.6 in the installation script.
April 2025
5 Commits • 3 Features
Apr 1, 2025April 2025 • Cedalion (ibs-lab/cedalion) monthly summary Key objective: deliver flexible GLM tooling, improve cross-platform reliability, and enhance documentation to empower users and reduce maintenance burden.
5 Commits • 3 Features
Apr 1, 2025April 2025 • Cedalion (ibs-lab/cedalion) monthly summary Key objective: deliver flexible GLM tooling, improve cross-platform reliability, and enhance documentation to empower users and reduce maintenance burden.
April 2025
March 2025
2 Commits
Mar 1, 2025March 2025 focused on robustness and maintainability in the cedalion repository, with two targeted bug fixes that enhance data reliability and user feedback. The work improves downstream data processing pipelines and reduces noise in logs, while maintaining compatibility with existing workflows.
March 2025
2 Commits
Mar 1, 2025March 2025 focused on robustness and maintainability in the cedalion repository, with two targeted bug fixes that enhance data reliability and user feedback. The work improves downstream data processing pipelines and reduces noise in logs, while maintaining compatibility with existing workflows.
February 2025
11 Commits • 5 Features
Feb 1, 2025February 2025 – Focused on strengthening data ingestion, modeling robustness, and visualization to deliver reliable scientific tooling and clearer signal interpretation. Key improvements across NIRS data handling, design matrix reliability, geometry registration, and visualization, with test coverage enhancing quality gates.
11 Commits • 5 Features
Feb 1, 2025February 2025 – Focused on strengthening data ingestion, modeling robustness, and visualization to deliver reliable scientific tooling and clearer signal interpretation. Key improvements across NIRS data handling, design matrix reliability, geometry registration, and visualization, with test coverage enhancing quality gates.
February 2025
January 2025
28 Commits • 10 Features
Jan 1, 2025January 2025 monthly summary for ibs-lab/cedalion focused on modernizing packaging and build tooling, enhancing GVTD reliability, expanding unit tests and data assets, and tightening CI/delivery workflows to improve reproducibility and business value.
January 2025
28 Commits • 10 Features
Jan 1, 2025January 2025 monthly summary for ibs-lab/cedalion focused on modernizing packaging and build tooling, enhancing GVTD reliability, expanding unit tests and data assets, and tightening CI/delivery workflows to improve reproducibility and business value.
December 2024
3 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for ibs-lab/cedalion: Delivered two major improvements that enhance build reliability and cross-implementation consistency. GaussianKernels alignment with Homer2, with a new GaussianKernelsWithTails variant to preserve the previous padding behavior, improves consistency for users migrating between implementations. BibTeX References Formatting Fixes ensure Sphinx/BibTeX builds run without errors by correcting an extra newline after the year and aligning entry types (including using @misc for @software). These changes reduce build failures, streamline onboarding, and improve developer experience. Technologies demonstrated include Python, Sphinx/BibTeX integration, and cross-implementation maintenance. Overall impact: more reliable builds, fewer support tickets, and smoother user migration between GaussianKernels and Homer2 implementations.
3 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for ibs-lab/cedalion: Delivered two major improvements that enhance build reliability and cross-implementation consistency. GaussianKernels alignment with Homer2, with a new GaussianKernelsWithTails variant to preserve the previous padding behavior, improves consistency for users migrating between implementations. BibTeX References Formatting Fixes ensure Sphinx/BibTeX builds run without errors by correcting an extra newline after the year and aligning entry types (including using @misc for @software). These changes reduce build failures, streamline onboarding, and improve developer experience. Technologies demonstrated include Python, Sphinx/BibTeX integration, and cross-implementation maintenance. Overall impact: more reliable builds, fewer support tickets, and smoother user migration between GaussianKernels and Homer2 implementations.
December 2024
November 2024
17 Commits • 7 Features
Nov 1, 2024November 2024 (2024-11) monthly summary for ibs-lab/cedalion: Key features delivered: - SNIRF CRS support: Add capability to specify Coordinate Reference System when reading SNIRF data by passing CRS through to geometry_from_probe, enabling geo-accurate analyses across datasets. - GLM and to_epochs enhancements: Extend GLM design matrix to permit averaging of short channels into a single regressor; improve to_epochs robustness across datasets (time units, interpolation, edge cases). - Pruning flexibility with flag_drop: Introduce flag_drop to prune_ch to choose between dropping pruned channels or setting them to NaN, increasing data handling flexibility. - Image reconstruction improvements: Refactor reconstruction flow to encapsulate flattening of channel/vertex dims and introduce apply_inv_sensitivity for inversion and application of sensitivity matrices; update related plots. - Photogrammetry notebooks enhancements: Add descriptive text, scalp plots for mapping validation, extended sticker-processing visuals, and non-interactive rendering to improve clarity and batch execution. - Development environment and dependencies: Update environment to include PyQt, ipympl, and updated core dependencies for compatibility and tooling. - Artifact generation and optical computations refactor: Refactor artifact generation to use a Protocol, remove mutable defaults, dynamically derive wavelengths in optical density calculations, and rename TDDR to tddr for PEP8 consistency. Major bugs fixed: - SNIRF data loading robustness: Fix handling of empty/malformed stimulus objects in SNIRF loading by validating 2D shape, logging a warning, and returning an empty DataFrame to prevent crashes. Overall impact and accomplishments: - Strengthened data integrity and reliability of SNIRF imports, enabling robust multi-dataset analyses. - Improved modeling fidelity and analysis pipeline resilience through GLM/to_epochs enhancements and dataset-agnostic robustness. - Increased flexibility in data curation and processing, better plotting and notebook usability, and smoother onboarding via updated development tooling. Technologies/skills demonstrated: - Python, data validation, and robust error handling in data loading. - GLM design and time-series processing, with improved epoch handling across datasets. - Photogrammetry tooling and notebook storytelling with mapping validation visuals. - Modern software engineering practices: Protocol-based design, PEP8 naming, dependency management, and refactoring for performance and readability. - Cross-discipline toolchain experience (PyQt, ipympl) and pipeline end-to-end improvements.
November 2024
17 Commits • 7 Features
Nov 1, 2024November 2024 (2024-11) monthly summary for ibs-lab/cedalion: Key features delivered: - SNIRF CRS support: Add capability to specify Coordinate Reference System when reading SNIRF data by passing CRS through to geometry_from_probe, enabling geo-accurate analyses across datasets. - GLM and to_epochs enhancements: Extend GLM design matrix to permit averaging of short channels into a single regressor; improve to_epochs robustness across datasets (time units, interpolation, edge cases). - Pruning flexibility with flag_drop: Introduce flag_drop to prune_ch to choose between dropping pruned channels or setting them to NaN, increasing data handling flexibility. - Image reconstruction improvements: Refactor reconstruction flow to encapsulate flattening of channel/vertex dims and introduce apply_inv_sensitivity for inversion and application of sensitivity matrices; update related plots. - Photogrammetry notebooks enhancements: Add descriptive text, scalp plots for mapping validation, extended sticker-processing visuals, and non-interactive rendering to improve clarity and batch execution. - Development environment and dependencies: Update environment to include PyQt, ipympl, and updated core dependencies for compatibility and tooling. - Artifact generation and optical computations refactor: Refactor artifact generation to use a Protocol, remove mutable defaults, dynamically derive wavelengths in optical density calculations, and rename TDDR to tddr for PEP8 consistency. Major bugs fixed: - SNIRF data loading robustness: Fix handling of empty/malformed stimulus objects in SNIRF loading by validating 2D shape, logging a warning, and returning an empty DataFrame to prevent crashes. Overall impact and accomplishments: - Strengthened data integrity and reliability of SNIRF imports, enabling robust multi-dataset analyses. - Improved modeling fidelity and analysis pipeline resilience through GLM/to_epochs enhancements and dataset-agnostic robustness. - Increased flexibility in data curation and processing, better plotting and notebook usability, and smoother onboarding via updated development tooling. Technologies/skills demonstrated: - Python, data validation, and robust error handling in data loading. - GLM design and time-series processing, with improved epoch handling across datasets. - Photogrammetry tooling and notebook storytelling with mapping validation visuals. - Modern software engineering practices: Protocol-based design, PEP8 naming, dependency management, and refactoring for performance and readability. - Cross-discipline toolchain experience (PyQt, ipympl) and pipeline end-to-end improvements.
Activity
Loading activity data...
Quality Metrics
Correctness90.2%
Maintainability90.4%
Architecture87.0%
Performance81.6%
AI Usage20.0%
Skills & Technologies
Programming Languages
BibTeXJSONJupyter NotebookMakefileMarkdownPytestPythonSQLShellTOML
Technical Skills
3D Plotting3D TransformationsAPI DesignAPI IntegrationAffine TransformationsBibTeXBrainstormBug FixingBuild AutomationBuild SystemBuild SystemsCAT12CI/CDCode FormattingCode Quality
Repositories Contributed To
Overview of all repositories you've contributed to across your timeline