ibs-lab/cedalion
Dec 2024 – May 2025
5 Months active
Languages Used
BibTeXPythonTSV
Technical Skills
Data AnalysisImage SegmentationMedical Image ProcessingNiBabelNumPyPython
nils
PROFILE
Nils
Nils Harmening contributed to the ibs-lab/cedalion repository by developing and refining data processing pipelines for neuroimaging and 3D head-model analysis. He implemented robust MRI segmentation post-processing and enhanced geometry handling, focusing on data integrity and reproducibility. Using Python, NumPy, and SciPy, Nils centralized normalization logic for 3D surface normals, improved TSV-based data ingestion with unit handling, and introduced new data structures for probe geometry. He addressed critical issues such as swapped fiducial landmarks and segmentation robustness, ensuring reliable downstream analyses. His work demonstrated depth in scientific computing, careful data correction, and a strong emphasis on maintainable, testable code.
Overall Statistics
Feature vs Bugs
67%Features
Repository Contributions
9Total
Bugs
3
Commits
9
Features
6
Lines of code
9,867
Activity Months5
Your Network
24 people
Work History
May 2025
1 Commits
May 1, 2025In May 2025, delivered a targeted data integrity fix in ibs-lab/cedalion to correct swapped fiducial landmarks for atlasviewer (RPA/LPA). The fix ensures accurate landmark identification by aligning labels and coordinates in two TSV files, preventing misinterpretation in landmark-based analyses and improving downstream reliability of atlasviewer workflows. This work enhances data quality for clinical and research pipelines relying on fiducial references and supports reproducible results across runs.
1 Commits
May 1, 2025In May 2025, delivered a targeted data integrity fix in ibs-lab/cedalion to correct swapped fiducial landmarks for atlasviewer (RPA/LPA). The fix ensures accurate landmark identification by aligning labels and coordinates in two TSV files, preventing misinterpretation in landmark-based analyses and improving downstream reliability of atlasviewer workflows. This work enhances data quality for clinical and research pipelines relying on fiducial references and supports reproducible results across runs.
May 2025
April 2025
1 Commits • 1 Features
Apr 1, 2025Month: 2025-04 — Focused feature delivery for ibs-lab/cedalion with robust TSV I/O enhancements and enhanced probe geometry support. No major bugs fixed this month.
April 2025
1 Commits • 1 Features
Apr 1, 2025Month: 2025-04 — Focused feature delivery for ibs-lab/cedalion with robust TSV I/O enhancements and enhanced probe geometry support. No major bugs fixed this month.
March 2025
5 Commits • 4 Features
Mar 1, 2025March 2025: Focused on robustness, data infrastructure, and head-model quality for cedalion. Delivered features enhanced data fidelity and usability, fixed critical crash scenarios, and aligned anatomical landmark placement with standardized systems to improve downstream analyses and decision-making. This work underpins reliable processing of UHD data, streamlined data pipelines, and more accurate tissue-property calculations, driving business value through better data-driven insights and reduced pipeline fragility.
5 Commits • 4 Features
Mar 1, 2025March 2025: Focused on robustness, data infrastructure, and head-model quality for cedalion. Delivered features enhanced data fidelity and usability, fixed critical crash scenarios, and aligned anatomical landmark placement with standardized systems to improve downstream analyses and decision-making. This work underpins reliable processing of UHD data, streamlined data pipelines, and more accurate tissue-property calculations, driving business value through better data-driven insights and reduced pipeline fragility.
March 2025
January 2025
1 Commits
Jan 1, 2025January 2025 monthly summary for ibs-lab/cedalion: Focused on improving robustness of 3D geometry processing by implementing robust vertex normal normalization in TrimeshSurface. Normals are now normalized before use and normalization logic is centralized in a dedicated method to improve stability when input vectors are not unit length. This reduces downstream errors in rendering and analysis and improves maintainability. The work is traceable to commit 023b09a2f09a1d8b72ea28f80d8baac30fe94f80 (fix optode_dirs if not perfectly unitary, #71).
January 2025
1 Commits
Jan 1, 2025January 2025 monthly summary for ibs-lab/cedalion: Focused on improving robustness of 3D geometry processing by implementing robust vertex normal normalization in TrimeshSurface. Normals are now normalized before use and normalization logic is centralized in a dedicated method to improve stability when input vectors are not unit length. This reduces downstream errors in rendering and analysis and improves maintainability. The work is traceable to commit 023b09a2f09a1d8b72ea28f80d8baac30fe94f80 (fix optode_dirs if not perfectly unitary, #71).
December 2024
1 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for ibs-lab/cedalion: Implemented MRI Segmentation Post-Processing Enhancement (SPM12) to refine segmentation outputs following Huang2013. Introduced a new post-processing function and removed an unused function to simplify the pipeline and improve data quality. The change enhances downstream neuroimaging analysis readiness and reduces manual cleanup.
1 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for ibs-lab/cedalion: Implemented MRI Segmentation Post-Processing Enhancement (SPM12) to refine segmentation outputs following Huang2013. Introduced a new post-processing function and removed an unused function to simplify the pipeline and improve data quality. The change enhances downstream neuroimaging analysis readiness and reduces manual cleanup.
December 2024
Activity
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Quality Metrics
Correctness86.6%
Maintainability86.6%
Architecture83.4%
Performance72.2%
AI Usage20.0%
Skills & Technologies
Programming Languages
BibTeXPythonTSV
Technical Skills
3D ModelingData AnalysisData CorrectionData EngineeringData HandlingData LoadingData OrganizationData ScienceData StructuresEnumFile Format ConversionFile I/OGeometry ProcessingImage ProcessingImage Segmentation
Repositories Contributed To
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