hael/SIMPLE
Nov 2024 – Nov 2025
13 Months active
Languages Used
FortrancmakeCMakeBashPython
Technical Skills
Algorithm OptimizationBug FixingCode CleanupCode RefactoringData AnalysisData Structures
cyrilr
PROFILE
Cyrilr
Cyril Reboul developed advanced 2D and 3D data processing pipelines for the hael/SIMPLE repository, focusing on robust streaming workflows, polar and symmetry-based reconstruction, and scalable clustering algorithms. Leveraging Fortran and Python, Cyril engineered features such as reference-based particle picking, memory-aware parallelization, and high-performance image processing to improve reconstruction accuracy and throughput. He implemented modular enhancements for multi-state analysis, optimized file I/O, and introduced automated testing utilities to ensure reliability. His work addressed complex challenges in scientific computing, delivering maintainable, cross-platform solutions that stabilized large-scale cryo-EM workflows and enabled reproducible, high-quality results across diverse computational environments.
Overall Statistics
Feature vs Bugs
62%Features
Repository Contributions
263Total
Bugs
52
Commits
263
Features
84
Lines of code
50,729
Activity Months13
Your Network
18 people
Work History
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.
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
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.
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.
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.
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
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.
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.
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.
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
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.
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.
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.
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
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.
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.
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.
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
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.
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.
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.
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
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.
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.
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.
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
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Quality Metrics
Correctness82.2%
Maintainability81.8%
Architecture77.0%
Performance70.4%
AI Usage20.0%
Skills & Technologies
Programming Languages
BashCMakeFortranPythoncmake
Technical Skills
3D Data Processing3D Processing3D ReconstructionAlgorithm DevelopmentAlgorithm ImplementationAlgorithm OptimizationAlgorithm RefinementAlgorithm TuningApplication ConfigurationArray IndexingBackend DevelopmentBioinformaticsBug FixBug FixingBuild System Configuration
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