SIMPLE
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Initializing search
hael/SIMPLE
SIMPLE
hael/SIMPLE
SIMPLE
SIMPLE hardware resource planning
Install
SIMPLE memory estimator and benchmark guide
Relocating project data
Algorithms
Algorithms
SIMPLE: the algorithms
Staged Ab Initio 2D Classification
Staged Ab Initio 3D Reconstruction
Automatic Gain-Reference Flip Detection
Cluster2D and CTF-Aware Class Averaging
Continuous In-Plane Refinement
CTF Modeling and Estimation
Projection-Aware Flex PCA
Multi-State Refinement and Reference-Guided Classification
Motion Correction
Nonuniform Filtering
NU-Evidence Envelope Masking
Particle Picking
Cartesian 3D Reconstruction
Iterative 3D Refinement
Probabilistic Pre-Alignment and Fractional Updates
Online Streaming Pipeline
Heterogeneity analysis
Heterogeneity analysis
Heterogeneity Analysis
Reference-Guided 3D Classification (classify3D_refs)
Projection-Aware Flex PCA
Conformational State Refinement (refine3D_states)
Code overview
Code overview
Fortran indexes
Fortran indexes
Api index
Module Index
Module Index
For developers
For developers
Preserving the Legacy In-Plane Path
Onboarding
Onboarding
SIMPLE Git Repo Onboarding
SIMPLE GUI Onboarding Guide
How2s
How2s
Processing heterogeneous data sets in SIMPLE
How to debug Fortran code
Useful GDB Commands
How2get code inventory
Useful Git Commands
Install FFTW
SLURM for beginners
SLURM job arrays
Implementation notes
Implementation notes
abinitio2D seeded restart: initialize from the previous 2D clustering
C-alpha finder
NU-Evidence Resolution Mask for C-alpha Detection
Standalone Cartesian pose refinement in refine3D
Continuous five-parameter pose refinement numerical validation
Continuous 3D refinement on the PCG operator: design note
Flex-generated 3D particle representatives for denoise_project
Dominant flex-density basin as a robust Bayesian 3D reconstruction estimator
flex_pca: sampling-distance control, reconstruction backends, and the envelope mask as solve support
NU-Evidence Envelope Masking
NU-evidence local sharpening: model-free LocScale from cross-half evidence
Retiring the NU shell walk: a dense static ladder with the regularized pair in the competition
The PCG reconstruction backend: what it is today
PCG backend: decision log
PCG backend: the complete experiment record (2026-08-25 to 2026-09-10)
Project data relocation implementation plan
Project data relocation specification
SINGLE on the PCG backend: the atomic density prior
Completed
Completed
Local-linear diffusion-map pre-image — validation plan
abinitio3D_addon — development proposal
Continuous 3-D pose refinement: consolidated history and handoff
Continuous 3-D pose refinement: consolidated scientific review
Continuous 3-D pose refinement: consolidated validation evidence
Continuous in-plane rotation transfer plan for refine3D
Continuous In-Plane Rotation Refinement
Continuous in-plane rotation in the polar representation (objfun=euclid)
Diffusion maps: lessons from a ManifoldEM review
Dropping the legacy box division from reconstruction output
Bug report: qsys job-completion detection
Reference-picker acceleration note
Policies
Policies
Internal Technical Memorandum
Coarray Execution Policy
FSC Area Score Policy
Importance Sampling and Fractional Update Policy
Microscope-Dependent Parameter Policy
Motion Gain Analysis Policy
Persistent Worker Policy
Phase-shift CTF Policy
Project Stack Indexing Policy
segdiampick_mics Policy
Test Environment Policy
UI Descriptor Layer Policy
2D
2D
Abinitio2D Policy
Class-Average Bootstrap Policy
Particle Cache Policy
3D
3D
abinitio3D_addon Policy
Abinitio3D Cavgs Policy
Abinitio3D Policy
Automasking Policy
Reference-Guided 3D Classification Policy
reconstruct3D PCG backend policy
Refine3D Auto Policy
Refine3D Policy
Separate alignment and reconstruction for multi-state peak-memory reduction
NU
NU
Nonuniform Filtering Policy
Heterogeneity
Heterogeneity
Conformational State Refinement Policy
Sieving and rejection
Sieving and rejection
Sieving and Rejection Policies
Class Compatibility Policy
Distance-Transform Shape Metrics for Class-Average Rejection
model_cavgs_rejection
Particle Sieve Policy
Refactoring notes
Refactoring notes
FLEX PCA architectural audit and staged refactoring plan
Canonical MRC stack and volume output suffix refactoring
Phase 5 of the test environment: handover to Ruben
SINGLE tests in the new test environment: handover to Ruben
Stream tests in the new test environment: handover to Ruben
Completed
Completed
Canonical Sigma2 State Refactoring
CMake Refactoring Migration Guide
Euclid Sigma Refactoring: Builder-Owned Policy
Initialize Poses Against External References Before Euclidean Refinement
Heterogeneity Analysis UI and Algorithm Documentation Refactoring
Refactoring: Merge Projects With Distinct CTF Models
NU filter high-resolution extension FT reuse
Phase-shift CTF support
Polar PFT Range Policy Refactor (2026-03-19)
Probabilistic alignment table peak-memory refactoring
Refactor Multi-State 3D Workflows Around Scientific Intent
Remove build_glob
Refactoring: Remove params_glob Global State
Refactoring Document: Global pftc_glob Removal
Retire the simple_reconstructor_eo Module
Test review record
SIMPLE's testing against modern practice: an assessment
UI Category Membership Tidying
A uniform, two-tier test environment for SIMPLE
Planned
Planned
Class-Average State and Reconstruct3D Partials Refactoring
The padded real-space array of image: zero padding, and a box-shaped pointer
Staged Domain-Driven Design Refactor
Adopting X's Execution Layer in SIMPLE
Rejected
Rejected
Abinitio3D SGD Refinement Implementation Plan
Contract/Implementation Module Architecture for Fast Builds
flex_analysis implementation plan
Refactoring Proposal: Exact-Projection Sparse Graphs for FLEX Analysis
User guide
User guide
update_project
User Guide
How2get code inventory
cloc $(git ls-files)