hael/SIMPLE
Nov 2024 – Apr 2026
18 Months active
Languages Used
FortrancmakeCMakeBashPythonMarkdown
Technical Skills
Algorithm OptimizationBug FixingCode CleanupCode RefactoringData AnalysisData Structures
cyrilr
PROFILE
Cyrilr
Cyril Reboul developed and maintained advanced 2D and 3D reconstruction pipelines for the hael/SIMPLE repository, focusing on robust streaming workflows, polar Fourier transform enhancements, and scalable clustering algorithms. Leveraging Fortran and Python, Cyril engineered features such as polar-based class averaging, reference-based particle picking, and memory-optimized image processing routines. His work included performance tuning, parallel computing strategies, and extensive bug fixing to ensure reliability and data integrity across large-scale cryo-EM datasets. Through iterative refactoring and modularization, Cyril improved maintainability and enabled rapid feature delivery, demonstrating deep technical understanding and a methodical approach to scientific software engineering challenges.
Overall Statistics
Feature vs Bugs
59%Features
Repository Contributions
371Total
Bugs
79
Commits
371
Features
116
Lines of code
84,392
Activity Months18
Your Network
18 peopleShared Repositories
18
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AtifMember
CaesarMember
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CaesarMember
CaesarMember
CaesarMember
Hans ElmlundMember
Work History
April 2026
4 Commits • 1 Features
Apr 1, 2026April 2026: Implemented Polar Fourier Transform enhancements in hael/SIMPLE, delivering a new polar interpolation scheme (pgrp=c1) with internal refactors and a patch to support trailing reconstruction with polar representation enabled. Also delivered memory-layout optimizations for polar coordinates (pftc%polar) and stability fixes to improve performance, reliability, and broader applicability of polar-based processing.
4 Commits • 1 Features
Apr 1, 2026April 2026: Implemented Polar Fourier Transform enhancements in hael/SIMPLE, delivering a new polar interpolation scheme (pgrp=c1) with internal refactors and a patch to support trailing reconstruction with polar representation enabled. Also delivered memory-layout optimizations for polar coordinates (pftc%polar) and stability fixes to improve performance, reliability, and broader applicability of polar-based processing.
April 2026
March 2026
32 Commits • 6 Features
Mar 1, 20262026-03 monthly highlights for hael/SIMPLE: Delivered polar handling and 3D restoration bug fixes, reinforcing centering accuracy for polar=yes and stabilizing ab initio3D workflows. Implemented performance optimizations across FFT normalization, estimate_lp_lim, and general filters, achieving meaningful speedups and better memory usage. Enhanced image processing with Fourier formulations and Gaussian filtering in pool2D, improving accuracy and throughput. Refined workflows with cluster2D and refine3D one-pass optimizations, reducing passes and increasing throughput. Achieved stabilization and reliability through targeted bug fixes (PSPEC, shared memory, compilation issues) and streaming improvements (dynreslim), enabling more robust runs on larger datasets. Technologies demonstrated: parallel computing, memory optimization, Fourier-based methods, Gaussian filtering, and resilient release engineering in ab initio pipelines.
March 2026
32 Commits • 6 Features
Mar 1, 20262026-03 monthly highlights for hael/SIMPLE: Delivered polar handling and 3D restoration bug fixes, reinforcing centering accuracy for polar=yes and stabilizing ab initio3D workflows. Implemented performance optimizations across FFT normalization, estimate_lp_lim, and general filters, achieving meaningful speedups and better memory usage. Enhanced image processing with Fourier formulations and Gaussian filtering in pool2D, improving accuracy and throughput. Refined workflows with cluster2D and refine3D one-pass optimizations, reducing passes and increasing throughput. Achieved stabilization and reliability through targeted bug fixes (PSPEC, shared memory, compilation issues) and streaming improvements (dynreslim), enabling more robust runs on larger datasets. Technologies demonstrated: parallel computing, memory optimization, Fourier-based methods, Gaussian filtering, and resilient release engineering in ab initio pipelines.
February 2026
33 Commits • 15 Features
Feb 1, 2026February 2026 monthly summary for hael/SIMPLE: Delivered a set of high-impact feature updates and stability fixes that advance 2D/3D reconstruction workflows, improve accuracy, and streamline builds. Key features include a major Classaverager overhaul using KB interpolation (new version and regularization of ab initio 2D final classes), Sigma2 interpolation utilities, gridding correction in reconstruction, and expanded cavg/interpolation options. Major bugs fixed spanned reconstructor reliability, 2D alignment, UI/2D components, and execution on queuing/streaming2D. Cross-cutting improvements encompassed API cleanup, memory pointer removals, and build consistency across compilers. Overall, the month improved robustness, performance, and flexibility of 2D/3D pipelines, enabling faster delivery and more configurable analyses.
33 Commits • 15 Features
Feb 1, 2026February 2026 monthly summary for hael/SIMPLE: Delivered a set of high-impact feature updates and stability fixes that advance 2D/3D reconstruction workflows, improve accuracy, and streamline builds. Key features include a major Classaverager overhaul using KB interpolation (new version and regularization of ab initio 2D final classes), Sigma2 interpolation utilities, gridding correction in reconstruction, and expanded cavg/interpolation options. Major bugs fixed spanned reconstructor reliability, 2D alignment, UI/2D components, and execution on queuing/streaming2D. Cross-cutting improvements encompassed API cleanup, memory pointer removals, and build consistency across compilers. Overall, the month improved robustness, performance, and flexibility of 2D/3D pipelines, enabling faster delivery and more configurable analyses.
February 2026
January 2026
13 Commits • 5 Features
Jan 1, 20262026-01 monthly summary for hael/SIMPLE: Delivered critical reliability fixes and substantial performance optimizations across the reconstruction and image-processing stack, with improved build configurability to support future ML capabilities and explicit performance tuning.
January 2026
13 Commits • 5 Features
Jan 1, 20262026-01 monthly summary for hael/SIMPLE: Delivered critical reliability fixes and substantial performance optimizations across the reconstruction and image-processing stack, with improved build configurability to support future ML capabilities and explicit performance tuning.
December 2025
26 Commits • 5 Features
Dec 1, 2025December 2025 monthly summary for hael/SIMPLE: Consolidated stability, performance, and maintainability improvements across the streaming and preprocessing pipeline. Delivered targeted features, completed a broad suite of bug fixes, and implemented refactors to improve code quality and future scalability. These efforts reduce risk, accelerate iteration, and support upcoming capabilities around PFT/MRC handling and 3D strategy behavior.
26 Commits • 5 Features
Dec 1, 2025December 2025 monthly summary for hael/SIMPLE: Consolidated stability, performance, and maintainability improvements across the streaming and preprocessing pipeline. Delivered targeted features, completed a broad suite of bug fixes, and implemented refactors to improve code quality and future scalability. These efforts reduce risk, accelerate iteration, and support upcoming capabilities around PFT/MRC handling and 3D strategy behavior.
December 2025
November 2025
11 Commits • 4 Features
Nov 1, 2025November 2025 performance summary for hael/SIMPLE: Delivered polar ab initio 3D reconstruction enhancements, robust particle picking improvements, TIFF-reading performance optimization, and robustness/fixes across import and sieving, complemented by code cleanup and memory-management improvements. These changes improved accuracy, processing reliability, and throughput, enabling more reliable 3D reconstructions and faster preprocessing.
November 2025
11 Commits • 4 Features
Nov 1, 2025November 2025 performance summary for hael/SIMPLE: Delivered polar ab initio 3D reconstruction enhancements, robust particle picking improvements, TIFF-reading performance optimization, and robustness/fixes across import and sieving, complemented by code cleanup and memory-management improvements. These changes improved accuracy, processing reliability, and throughput, enabling more reliable 3D reconstructions and faster preprocessing.
October 2025
32 Commits • 13 Features
Oct 1, 2025Monthly summary for 2025-10 focused on delivering robust data processing features, stabilization of pipelines, and enabling larger-scale analyses in hael/SIMPLE. Delivered major feature work across centering, polar clustering, ab initio workflows, and mini-stream processing, alongside targeted bug fixes and test scaffolding to improve reliability and maintainability. Business value centers on higher reconstruction quality, faster I/O, and scalable preprocessing for larger datasets.
32 Commits • 13 Features
Oct 1, 2025Monthly summary for 2025-10 focused on delivering robust data processing features, stabilization of pipelines, and enabling larger-scale analyses in hael/SIMPLE. Delivered major feature work across centering, polar clustering, ab initio workflows, and mini-stream processing, alongside targeted bug fixes and test scaffolding to improve reliability and maintainability. Business value centers on higher reconstruction quality, faster I/O, and scalable preprocessing for larger datasets.
October 2025
September 2025
19 Commits • 2 Features
Sep 1, 2025September 2025 monthly summary for hael/SIMPLE: Delivered consolidated polar workflow and symmetry enhancements across ab initio and refine3D, along with memory and stability improvements that strengthen reliability of end-to-end pipelines. Key deliverables include: (1) Polar workflow and symmetry enhancements for ab initio and refine3D, including cleanup of polar parameter handling, simplified mirror operations, improved support for polar representations in ab initio3D/2D workflows, GAUREF control refinements, and performance-oriented polar update optimizations. (2) 2D class averaging and streaming enhancements with testing options for abinitio2D (frequency marching, new cc objective), interactive sieve selection, and improved 2D particle sampling. (3) Stability and memory management improvements with explicit deallocation and resource cleanup in abinitio2D_stream and related components, plus consistent data filtering/cleanup. (4) 3D refinement correctness fixes and UI filter reliability, addressing shift parameter assignments in symmetry search, improved sigma handling in 3D refinement, and fixes to the UI filter "required" behavior. These efforts collectively reduce runtime, improve reliability, and enable more reproducible results in ab initio and refinement workflows.
September 2025
19 Commits • 2 Features
Sep 1, 2025September 2025 monthly summary for hael/SIMPLE: Delivered consolidated polar workflow and symmetry enhancements across ab initio and refine3D, along with memory and stability improvements that strengthen reliability of end-to-end pipelines. Key deliverables include: (1) Polar workflow and symmetry enhancements for ab initio and refine3D, including cleanup of polar parameter handling, simplified mirror operations, improved support for polar representations in ab initio3D/2D workflows, GAUREF control refinements, and performance-oriented polar update optimizations. (2) 2D class averaging and streaming enhancements with testing options for abinitio2D (frequency marching, new cc objective), interactive sieve selection, and improved 2D particle sampling. (3) Stability and memory management improvements with explicit deallocation and resource cleanup in abinitio2D_stream and related components, plus consistent data filtering/cleanup. (4) 3D refinement correctness fixes and UI filter reliability, addressing shift parameter assignments in symmetry search, improved sigma handling in 3D refinement, and fixes to the UI filter "required" behavior. These efforts collectively reduce runtime, improve reliability, and enable more reproducible results in ab initio and refinement workflows.
August 2025
21 Commits • 8 Features
Aug 1, 2025Concise monthly summary for 2025-08 focusing on delivering value through feature enhancements, performance improvements, and robust bug fixes across the SIMPLE repository. Highlights include major improvements to 3D and 2D streaming pipelines, polar processing optimizations, and a set of stability fixes that enhance data integrity and processing throughput.
21 Commits • 8 Features
Aug 1, 2025Concise monthly summary for 2025-08 focusing on delivering value through feature enhancements, performance improvements, and robust bug fixes across the SIMPLE repository. Highlights include major improvements to 3D and 2D streaming pipelines, polar processing optimizations, and a set of stability fixes that enhance data integrity and processing throughput.
August 2025
July 2025
27 Commits • 5 Features
Jul 1, 2025July 2025 summary for hael/SIMPLE focused on delivering a robust streaming workflow, stabilizing polar analysis pipelines, and expanding 2D/3D clustering capabilities, while improving deployment hygiene and configuration management. The month emphasized business value through faster iteration, more reliable reconstructions, and easier maintenance. Key actions included a major streaming implementation refactor with cluster2D_subsets enhancements, extensive polar CAVG bug fixes, 3D polar reference and interpolation improvements, common line interpolation enhancements with mirroring geometry, and deployment/CLI improvements plus a draft configuration file to streamline experiments.
July 2025
27 Commits • 5 Features
Jul 1, 2025July 2025 summary for hael/SIMPLE focused on delivering a robust streaming workflow, stabilizing polar analysis pipelines, and expanding 2D/3D clustering capabilities, while improving deployment hygiene and configuration management. The month emphasized business value through faster iteration, more reliable reconstructions, and easier maintenance. Key actions included a major streaming implementation refactor with cluster2D_subsets enhancements, extensive polar CAVG bug fixes, 3D polar reference and interpolation improvements, common line interpolation enhancements with mirroring geometry, and deployment/CLI improvements plus a draft configuration file to streamline experiments.
June 2025
20 Commits • 9 Features
Jun 1, 2025June 2025 monthly summary for hael/SIMPLE focusing on delivering a robust polar processing pipeline and 2D/3D workflows, with notable improvements in defocus pruning, junk-class detection, and clustering robustness. Built compatibility with g++ 15 and updated documentation. Emphasis on data integrity, performance, and maintainability.
20 Commits • 9 Features
Jun 1, 2025June 2025 monthly summary for hael/SIMPLE focusing on delivering a robust polar processing pipeline and 2D/3D workflows, with notable improvements in defocus pruning, junk-class detection, and clustering robustness. Built compatibility with g++ 15 and updated documentation. Emphasis on data integrity, performance, and maintainability.
June 2025
May 2025
20 Commits • 5 Features
May 1, 2025May 2025 summary for hael/SIMPLE focused on delivering robust multi-chunk analysis, enhanced class averaging, and state-aware reconstruction workflows. Implemented unified cavgs across chunked cluster2D_subsets, improved particle/class metadata mapping, and expanded post-processing outputs (frcs) to streamline multi-chunk results. Introduced junk detection and normalization to stabilize class averages, advanced multi-state averaging with state-aware metadata handling, and added weighting, labeling, and Gaussian filtering for improved convergence and accuracy. Polar coordinate representations and PFT enhancements were refined to support richer polar analysis. Fixed critical bugs in ICM filtering, projection checks, and logging to stabilize the pipeline, collectively reducing rework and accelerating downstream reconstruction and analytics.
May 2025
20 Commits • 5 Features
May 1, 2025May 2025 summary for hael/SIMPLE focused on delivering robust multi-chunk analysis, enhanced class averaging, and state-aware reconstruction workflows. Implemented unified cavgs across chunked cluster2D_subsets, improved particle/class metadata mapping, and expanded post-processing outputs (frcs) to streamline multi-chunk results. Introduced junk detection and normalization to stabilize class averages, advanced multi-state averaging with state-aware metadata handling, and added weighting, labeling, and Gaussian filtering for improved convergence and accuracy. Polar coordinate representations and PFT enhancements were refined to support richer polar analysis. Fixed critical bugs in ICM filtering, projection checks, and logging to stabilize the pipeline, collectively reducing rework and accelerating downstream reconstruction and analytics.
April 2025
21 Commits • 8 Features
Apr 1, 2025April 2025 monthly summary (Month: 2025-04) for hael/SIMPLE. Focused on stabilizing streaming and processing pipelines, extending 2D/3D reconstruction capabilities, and hardening the system against race conditions. Key deliverables include Abinitio3D streaming improvements and targeted fixes (volumes alignment and scoring), a major core processing bugfix that stabilized performance, progress on Cluster2D streaming/autosampling, and targeted multistate enhancements to abinitio3D cavs along with reconstruction race-condition fixes. Additional reliability work covered streaming 2D fixes and supporting bugfixes (reproject, pspecs) to reduce downtime and improve accuracy. Overall impact: more reliable streaming, faster iteration, and expanded multistate capabilities enabling more accurate reconstructions across pipelines.
21 Commits • 8 Features
Apr 1, 2025April 2025 monthly summary (Month: 2025-04) for hael/SIMPLE. Focused on stabilizing streaming and processing pipelines, extending 2D/3D reconstruction capabilities, and hardening the system against race conditions. Key deliverables include Abinitio3D streaming improvements and targeted fixes (volumes alignment and scoring), a major core processing bugfix that stabilized performance, progress on Cluster2D streaming/autosampling, and targeted multistate enhancements to abinitio3D cavs along with reconstruction race-condition fixes. Additional reliability work covered streaming 2D fixes and supporting bugfixes (reproject, pspecs) to reduce downtime and improve accuracy. Overall impact: more reliable streaming, faster iteration, and expanded multistate capabilities enabling more accurate reconstructions across pipelines.
April 2025
March 2025
18 Commits • 5 Features
Mar 1, 2025March 2025 monthly summary for hael/SIMPLE focusing on business value, technical achievements, and cross-platform readiness. Major work centered on Abinitio 3D streaming enablement, 2D sampling/clustering enhancements, and platform/build improvements, with targeted bug fixes to preserve data integrity across streaming stacks.
March 2025
18 Commits • 5 Features
Mar 1, 2025March 2025 monthly summary for hael/SIMPLE focusing on business value, technical achievements, and cross-platform readiness. Major work centered on Abinitio 3D streaming enablement, 2D sampling/clustering enhancements, and platform/build improvements, with targeted bug fixes to preserve data integrity across streaming stacks.
February 2025
19 Commits • 2 Features
Feb 1, 2025February 2025 monthly summary for hael/SIMPLE: Delivered substantial enhancements to the 2D classification and sampling framework, enabling higher accuracy and more flexible sampling with autosampling, improved statistics output, and enhanced particle mapping. Introduced new sampling parameters, deprecations, and streamlined assignment logic to simplify workflows. Fixed a set of critical bugs in 2D processing and probability table generation, including shared memory execution, dynamic resolution flow, indexing in probability tables, and initialization logic, stabilizing offline and streaming classifications. Advanced image transformation capabilities with Fourier-based alignment improvements, mirroring with Fourier center preservation, and additional testing utilities to validate transforms. These efforts collectively improve robustness, speed, and reliability of 2D analysis pipelines, delivering measurable business value in data quality and processing throughput. Technologies/skills demonstrated: Python-based 2D image processing, memory-aware parallelization (shared memory), Fourier-based transforms, testing frameworks, code maintainability, and CI-ready releases.
19 Commits • 2 Features
Feb 1, 2025February 2025 monthly summary for hael/SIMPLE: Delivered substantial enhancements to the 2D classification and sampling framework, enabling higher accuracy and more flexible sampling with autosampling, improved statistics output, and enhanced particle mapping. Introduced new sampling parameters, deprecations, and streamlined assignment logic to simplify workflows. Fixed a set of critical bugs in 2D processing and probability table generation, including shared memory execution, dynamic resolution flow, indexing in probability tables, and initialization logic, stabilizing offline and streaming classifications. Advanced image transformation capabilities with Fourier-based alignment improvements, mirroring with Fourier center preservation, and additional testing utilities to validate transforms. These efforts collectively improve robustness, speed, and reliability of 2D analysis pipelines, delivering measurable business value in data quality and processing throughput. Technologies/skills demonstrated: Python-based 2D image processing, memory-aware parallelization (shared memory), Fourier-based transforms, testing frameworks, code maintainability, and CI-ready releases.
February 2025
January 2025
22 Commits • 8 Features
Jan 1, 2025January 2025 (Month: 2025-01) focused on delivering robust features for 2D/3D classification workflows, improving core reliability, and expanding cross‑hardware support. Key features delivered include ring‑shaped picking improvements with membrane patch shape handling and selection updates, a probability table framework for 2D classification, and new ab initio 3D cluster sampling capabilities. In addition, streaming pathways were enhanced with automated resolution limit testing to improve end‑to‑end throughput. Platform portability was advanced through Silicon M3/M3Pro compilation fixes, enabling broader hardware deployment.
January 2025
22 Commits • 8 Features
Jan 1, 2025January 2025 (Month: 2025-01) focused on delivering robust features for 2D/3D classification workflows, improving core reliability, and expanding cross‑hardware support. Key features delivered include ring‑shaped picking improvements with membrane patch shape handling and selection updates, a probability table framework for 2D classification, and new ab initio 3D cluster sampling capabilities. In addition, streaming pathways were enhanced with automated resolution limit testing to improve end‑to‑end throughput. Platform portability was advanced through Silicon M3/M3Pro compilation fixes, enabling broader hardware deployment.
December 2024
13 Commits • 6 Features
Dec 1, 2024December 2024 highlights for hael/SIMPLE focusing on performance, correctness, and scalability. Delivered feature-rich PSpec workflow improvements, multi-state processing, and streaming enhancements, along with targeted reliability fixes that improve data quality, throughput, and production readiness. The work enables larger datasets, more complex state configurations, and more maintainable code.
13 Commits • 6 Features
Dec 1, 2024December 2024 highlights for hael/SIMPLE focusing on performance, correctness, and scalability. Delivered feature-rich PSpec workflow improvements, multi-state processing, and streaming enhancements, along with targeted reliability fixes that improve data quality, throughput, and production readiness. The work enables larger datasets, more complex state configurations, and more maintainable code.
December 2024
November 2024
20 Commits • 9 Features
Nov 1, 2024November 2024 performance summary for hael/SIMPLE. Delivered robustness improvements, streaming workflow overhauls, and expanded analysis capabilities. Key work includes enforcing integer types for numerical precision across particle/field handling, absolute path handling for reliable IO, overhauls to Ab Initio 2D streaming and classification, enhancements to docking interpolation, and modularization of motion correction utilities. Implemented comprehensive bug fixes across core algorithms (center calculations, ice fraction, denoising, lpset handling, abinitio3D parts) to improve stability and data integrity. Result: more reliable simulations, scalable pipelines, faster feature delivery, and clearer traceability via commits.
November 2024
20 Commits • 9 Features
Nov 1, 2024November 2024 performance summary for hael/SIMPLE. Delivered robustness improvements, streaming workflow overhauls, and expanded analysis capabilities. Key work includes enforcing integer types for numerical precision across particle/field handling, absolute path handling for reliable IO, overhauls to Ab Initio 2D streaming and classification, enhancements to docking interpolation, and modularization of motion correction utilities. Implemented comprehensive bug fixes across core algorithms (center calculations, ice fraction, denoising, lpset handling, abinitio3D parts) to improve stability and data integrity. Result: more reliable simulations, scalable pipelines, faster feature delivery, and clearer traceability via commits.
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Quality Metrics
Correctness83.4%
Maintainability82.0%
Architecture78.6%
Performance74.2%
AI Usage21.2%
Skills & Technologies
Programming Languages
BashCMakeFortranMarkdownPythoncmake
Technical Skills
2D clustering3D Data Processing3D Processing3D Reconstruction3D graphics programming3D modeling3D reconstructionAlgorithm DevelopmentAlgorithm ImplementationAlgorithm OptimizationAlgorithm RefinementAlgorithm TuningApplication ConfigurationArray IndexingBackend Development
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