Development Builds

Latest development builds from the staging branch. These are pre-release builds for testing.

MNE-CPP v2.3.0

Highlights

• MNE Inspect multimodal visualization — Unified MultimodalScene integrating sEEG depth electrodes, ECoG grids/strips (ElectrodeObject), MRI orthogonal slices (SliceObject), cortical surfaces with STC overlays, dipoles, connectivity arcs, and sensor locations; cross-modality picking with shared PickResult and timeline; data-driven colormap controls.
• MNE Scan production hardening — Plugin audit, real-time CMNE wiring (MNE/dSPM/sLORETA/CMNE method selector), recording/replay/resume, quickstart/hardware/deployment documentation, packaging refinements.
• MNE Analyze cortical workflow — FreeSurfer surface plugin, STC overlay with threshold/mid/max colormap and time slider, vertex picking and timecourse display.
• MNE Align coregistration wizard — 7-step wizard-guided coregistration tool with Polhemus FASTRAK serial driver, fiducial/HSP/EEG-cap digitization, Kabsch SVD + ICP alignment, -trans.fif export; session persistence; optical calibration engine with constrained solver.
• Video overlay & probe tracking — Tracker-driven video overlay projection on head surface with billboard fallback and vertex-displaced depth relief; catheter probe visualization (station 3) with tip-only crosshair, glow aura, and ethereal instrument shader.
• MRI slice rendering — 3D orthogonal MRI slice rendering with per-viewport visibility, intensity windowing controls, voxel-to-world transforms, and session persistence.
• MNE-Python algorithm parity (~92%) — Covariance estimation (auto/shrunk/OAS/FA/PCA), inverse convenience API, preprocessing & artifact detection, standard montages (10-20/10-10/10-05), Maxwell movement compensation, multitaper TFR, Picard ICA, surface Laplacian, auto ICA classification, depth priors, resolution metrics, SourceMorph, TRAP-MUSIC, TF-MxNE, CSP/SPoC/SSD decoding, simulation API.
• Skigen integration — ML algorithms (StandardScaler, MinMaxScaler, LOF, LedoitWolf, OAS, EmpiricalCovariance, FactorAnalysis, CSP, SPoC, SSD) delegated to skigen; API provenance registry with CI validation.
• SPDX license-header normalization — 1013 files migrated to unified SPDX+Doxygen headers; CI gate enforces compliance on every PR.
• Doxygen-to-Docusaurus API docs — Complete automated pipeline (doxy2mdx.py) generating 355 MDX pages (336 classes + 19 library indexes) with Mermaid inheritance diagrams and cross-reference hyperlinks.

New Features

• Covariance estimation parity (TASK 12): Auto/shrunk/OAS/FA/PCA/regularize/whitener methods; apply_inverse_epochs/raw/cov, beamformer epochs, source PSD/power convenience API
• Preprocessing & artifact detection parity (TASK 13): Maxwell bad-channel detection, EOG regression, EEG re-referencing, cHPI filter, stim artifact removal, muscle/amplitude annotation, bridged electrode detection, LOF bad-channel detection, fine calibration, annotation↔event conversion
• Source estimate types (TASK 14): VectorSourceEstimate, VolSourceEstimate, MixedSourceEstimate; label operations (extract_label_time_course with 5 modes, stc↔label, grow/split labels)
• Decoding (TASK 15): CSP/SPoC/SSD/SlidingEstimator/GeneralizingEstimator/ReceptiveField; I/O export (EDF/BrainVision), AEC/PEC connectivity, HTML Report, linear regression, RM-ANOVA, bootstrap CI, fixed-length epochs
• Standard montages (TASK 6): 10-20/10-10/10-05 electrode montage support
• Maxwell movement compensation (TASK 6): Full Maxwell filter movement compensation
• Multitaper TFR (TASK 7): Multitaper time-frequency representation
• Picard ICA (TASK 7): Picard-based ICA decomposition algorithm
• Surface Laplacian (TASK 7): Current source density via surface Laplacian
• Auto ICA classification (TASK 7): Automated ICA component labeling
• Depth priors & resolution metrics (TASK 8): PSF/CTF resolution metrics for source estimation
• Full SourceMorph (TASK 8): Complete cross-subject cortical morphing
• TRAP-MUSIC (TASK 8): TRAP-MUSIC source localization algorithm
• TF-MxNE (TASK 6): Time-frequency mixed-norm estimates
• Simulation API (TASK 9): simulate_raw/_stc/_evoked, addNoise/Ecg/Eog/Chpi in new sim library
• MNE Inspect plugins: Electrode visualization plugin (inspect_electrodes), MRI slices plugin (inspect_mri_slices)
• MNE Analyze Studio skills: MNA-aware agent skills extension (mna_skills)
• MNE Analyze cortical surface plugin: STC load with fThresh/fMid/fMax colormap, time slider, play/pause
• Real-time CMNE: CMNE method added to MNE Scan minimum norm settings (combo: MNE/dSPM/sLORETA/CMNE) with model-checkpoint picker
• Polhemus FASTRAK driver: Serial backend with auto-detection, pivot calibration, optical path calibration engine, Kabsch SVD registration with vertex disambiguation
• NIfTI reader: NIfTI-1 single-file reader (.nii/.nii.gz) for MRI slice plugins
• Documentation screenshot tool: mne_doc_shots manifest-driven screenshot generation for manual pages
• macOS .dmg generation: create-dmg integration with codesign and notarization hooks
• API provenance registry: doc/api_registry.json with 90+ entries; tools/validate_api_registry.py CI validation

MNE Inspect

• Multimodal visualization — Integrated MultimodalScene with electrode, MRI slice, brain surface, STC overlay, dipole, connectivity, and sensor renderables
• Electrode plugin — sEEG depth electrodes and ECoG grid/strip visualization with instanced contact spheres
• MRI slices plugin — 3D orthogonal MRI slice rendering with per-viewport visibility, intensity windowing controls, voxel-to-world transforms, and session persistence
• Video overlay — Tracker-driven video texture projection on head surface with billboard fallback and vertex-displaced depth relief
• Probe tracking — Catheter probe visualization (station 3) with tip-only rotating crosshair, glow aura, and ethereal instrument shader

MNE Scan

• Real-time CMNE — Cascaded MNE method added to minimum norm plugin with MNE/dSPM/sLORETA/CMNE selector and ONNX model-checkpoint picker
• Quickstart documentation — Hardware setup, deployment, and quickstart manual pages

MNE Align

• New coregistration application — 7-step wizard: Load FIFF digitizer points → Verify → Acquire fiducials → Acquire head shape → Acquire EEG cap → ICP alignment → Save -trans.fif
• Polhemus FASTRAK integration — Live serial acquisition with auto-detect, pivot calibration, hemisphere configuration
• 3D visualization — Interactive BrainView with signal-driven sync, session persistence, marker rendering
• Session persistence — Full save/restore of coregistration state including acquired points and nested group prefixes
• Optical calibration — Constrained solver with known tracker-to-objective distance, sample persistence, direct objective center capture

Skigen Integration

• Delegated algorithms: StandardScaler, MinMaxScaler, LOF, LedoitWolf, OAS, EmpiricalCovariance, FactorAnalysis, CSP, SPoC, SSD
• Policy: Never reimplement sklearn algorithms in mne-cpp; implement in skigen first
• Init scripts: Updated init.sh/init.bat to clone skigen automatically
• CI: API registry validation workflow

CI/CD

• Fixed polyglot .bat SPDX headers causing bash syntax errors on Linux/macOS — REM Copyright (c) replaced with :;# comment style valid in both shells
• Fixed mne_doc_shots link errors on Linux with code coverage (__gcov_exit unresolved) — added --coverage compile/link flags
• Fixed mne_doc_shots MSVC RuntimeLibrary mismatch on Windows (MD_DynamicRelease vs MT_StaticRelease) — set MSVC_RUNTIME_LIBRARY to match project libraries
• Added SPDX license-header CI gate (license-headers.yml)
• Added API registry validation CI gate (api-registry-validate.yml)
• Added Doxygen API docs CI pipeline (api-docs.yml)
• Added screenshot regression CI (screenshot-regression.yml)
• Fixed CI deploy auth: replaced expired GIT_CREDENTIALS with GH_PAT
• Fixed Linux Qt builds: added XKB/XCB/EGL/GLES dev library dependencies
• Fixed Windows CI: use vswhere for VS toolchain discovery
• Fixed macOS CI: clear stale pip cache before setup-python
• Fixed 15 pipeline annotations in staging/codeql workflows
• Removed broken auto-fix-build workflow
• Consolidated license-headers workflow into staging pipeline
• Qt 6.11.1 toolchain across all CI workflows

Documentation

• SPDX license headers: 1013 files migrated to unified SPDX+Doxygen format with chronological author order and rename history
• Doxygen API docs pipeline: tools/doxy2mdx/doxy2mdx.py (1394 lines) generating 355 MDX pages with Mermaid inheritance diagrams, XML-backed cross-references, and per-library indexes
• MNE Align manual (mne-align.mdx): 7-step wizard documentation
• MNE Scan manual (mne-scan-hardware.mdx, mne-scan-quickstart.mdx, mne-scan-deployment.mdx): 18 plugins enumerated
• MNE Analyze Studio manual (mne-analyze-studio.mdx): Agent-based workflow documentation
• MNE Inspect multimodal manual (mne-inspect-multimodal.mdx): Multimodal visualization guide
• Build guide: Updated for init-script workflow, Skigen dependency, and script paths
• API sidebar: Restructured — Namespaces/Classes/Files/Hierarchy/Members nested under Overview category
• Thin-plate-spline warp example (Closes #475)

Refactoring

• Renamed conn library to connectivity to match mne-python naming
• Removed redundant null checks before delete (Closes #857)
• Modernized header format: unified v3 SPDX+Doxygen with @author/@since/@date tags
• Renamed FastTrak → Fastrak (correct product name)

Bug Fixes

• Fixed QWARN deprecation warnings in test_mne_io_coverage (replaced with qWarning())
• Fixed FIFF coordinate transformations: retain a...

MNE-CPP v2.2.1

Bug Fixes

• mne_inspect — STC scrolling broken on desktop (regression introduced in 2.2.0). Scrubbing the STC time-slider froze playback, produced flicker / "stretched-triangle" geometry artefacts, and could crash the application after a few seconds.
  • Root cause: commit b58c18a8c2 ("Energy/computational savings…") switched the per-surface vertex buffer from QRhiBuffer::Immutable to QRhiBuffer::Dynamic to enable in-place colour updates. Dynamic is documented for small, frequently-updated payloads (UBOs, a few hundred bytes); using it for a multi-MB brain-surface VBO triggers two failure modes on Metal/Vulkan:
    1. Each in-flight frame slot keeps its own physical buffer. Skipping the per-frame updateDynamicBuffer() (because m_gpu->dirty was false) caused the GPU to sample the wrong slot — visible as stuck frames and wildly out-of-range vertex positions.
    2. Allocating a 4-5 MB Dynamic buffer × in-flight slots × every visible surface multiplied GPU memory pressure by roughly 3×, leading to allocation failures during interactive scrubbing.
  • The WebAssembly build was unaffected because the WASM merged-surface renderer uses Immutable buffers re-uploaded every frame.
  • Fix: revert just the desktop VBO type to QRhiBuffer::Immutable (re-created when vertex data is dirty). All other improvements from b58c18a8c2 (demand-driven render, cached vertex count, IBO upload gating, removal of redundant updateBuffers in renderSurface) are kept.
  • Files: src/libraries/disp3D/renderable/brainsurface.cpp.

MNE-CPP v2.2.0

What's Changed

Highlights

• MNX as MNE Scan project storage — Pipeline configurations now load and save as .mna (JSON) or .mnx (CBOR) files via MnaIO; legacy XML pipeline format removed. Default auto-save path is default.mna.
• Unified File-menu naming across applications — mne_scan, mne_inspect, and mne_browse now use the same "Open Project… / Save Project… / Export Project as MNX…" pattern.
• MNE-C CLI parity (82 tools) — every command-line tool from MNE-C has a mne-cpp counterpart; final 4 ports landed in this release (mne_make_movie, mne_convert_lspcov, mne_convert_ncov, mne_dacq_annotator).
• Lossless MNA / MNX round-trip — every MNA struct preserves unknown JSON/CBOR keys via an extras field, so newer schema fields survive a round-trip through older software.
• Performance as a co-equal optimization goal — periodic code-optimization prompt and matching optimization-requirements.md doc cover both idiomatic-code refactors and quantitative perf wins (≥ 5 % wall-clock).

New Features

• MNA graph-execution library (mne_mna): New library for the .mna analysis node-graph format with YAML-based operator definitions, topological execution, and MnaOpRegistry for built-in and user-registered operators
• MNX binary container — CBOR-based binary equivalent of .mna (MNX1 magic header), with embedded-data support and identical key structure for lossless format conversion
• MNA Scan integration — MnaGraph m_pPipelineGraph mirrors the live plugin scene in PluginSceneManager; MnaDataKind ↔ ConnectorDataType mapping shipped in mna_scan_types; PluginGui::loadConfig/saveConfig route through MnaIO::read/MnaIO::write
• Stream-mode MnaGraphExecutor — MnaGraphExecutor::startStream() / stopStream() with StreamContext for real-time acquisition pipelines
• Machine-learning library (mne_ml): New library with MlTrainer for sklearn-compatible model training via embedded Python, supporting SVM, Random Forest, Logistic Regression, and custom estimators
• STS covariance estimators: Added Ledoit-Wolf and Oracle Approximating Shrinkage (OAS) estimators to the sts library with cross-validation support against scikit-learn
• Source-space cluster permutation tests — StatsCluster::oneSamplePermutationTest(), fTestPermutationTest(), tfce() (threshold-free cluster enhancement); StatsAdjacency::fromSourceSpaceTemporal() for spatio-temporal adjacency
• Spectral connectivity expansion — GrangerCausality ("GC"), DirectedTransferFunction ("DTF"), PartialDirectedCoherence ("PDC"); shared MVAR fitting via MvarModel
• CMNE sparse inverse: Added Cascaded MNE (InvCMNE) solver to the inverse library for spatially sparse source estimation
• DSP Infomax ICA: Extended the dsp library with an Infomax-based ICA decomposition algorithm
• BIDS coordinate system: Added BidsCoordinateSystem class for round-trip parsing and writing of coordinatesystem.json, and BidsElectrode::toFiffDigPoints() for converting BIDS electrodes to FIFF digitizer point sets
• FreeSurfer atlas lookup: Added FsAtlasLookup for Desikan-Killiany / Destrieux atlas region querying
• MRI slicer: Added MriSlicer class for extracting orthogonal slices (Axial/Sagittal/Coronal) from NIfTI volumes
• 3D electrode visualization: ElectrodeObject now includes QRhi GPU buffer management (updateBuffers, vertexBuffer, indexBuffer, instanceBuffer) following the BrainSurface pattern; new electrode.vert / electrode.frag shaders with instanced contact spheres and Blinn-Phong lighting
• 3D MRI slice visualization: New SliceObject renderable for textured MRI volume slices with voxel-to-world transforms and intensity windowing; new slice.vert / slice.frag shaders
• FiffAnnotations integration: AnnotationModel refactored to use FiffAnnotations as backing store instead of internal QVector<AnnotationEntry>, with fiffAnnotations() / setFiffAnnotations() public accessors
• Python cross-validation tests: Added GUARD_PYTHON / GUARD_PYTHON_PACKAGE macros ensuring Python-dependent tests fail in CI (MNE_REQUIRE_PYTHON=true) instead of silently skipping
• PythonTestHelper extensions: Added writeMatrix(), readMatrix(), and evalMatrixViaFile() convenience methods for Eigen↔NumPy round-trip validation
• MNA Scan plugin registry: Added scan-plugins.json schema and MnaScanTypes class for declaring MNE Scan plugins as MNA operator schemas
• W-file I/O: Added read_w and write_w methods to FiffStream for FreeSurfer .w format surface data
• Cortical surface mapping: New MNECorticalMap class with icoDownsample() for icosahedral downsampling, smoothOperator() for nearest-neighbor surface smoothing, and computeMorphMaps() for cross-subject cortical morphing
• Scalp surface generation: Added makeScalpSurfaces() to MNEBemSurface for creating decimated scalp meshes at multiple resolutions
• Processing history: Added copyProcessingHistory() to FiffStream for transferring processing provenance between FIFF files

MNE Inspect

• UI overhaul — Native QMenuBar (File / View / Tools / Help) with macOS system-menu integration, Recent Projects submenu (max 10), Ctrl+O / Ctrl+Q / Space shortcuts; closable + movable Controls and Loaded Files dock widgets with custom flat title bars; status bar with progress; saveState() / restoreState() persistence
• Loaded Files panel — live QTreeWidget with Name / Type / Path columns and context menu (Remove, Copy Path, Show in Finder); double-click STC entry activates it in the source-estimate combo
• Progressive-disclosure controls — load buttons removed from sidebar; menu actions are the single entry point; control groups disabled until matching data loads; data unload via Loaded Files context menu
• WASM compatibility — menu bar renders inline; QFileDialog guarded for WASM; recent-files menu disabled on WASM

MNE Scan

• File menu uses Project terminology — &New Project (Ctrl+N), &Open Project… (Ctrl+O, accepts *.mna *.mnx), &Save Project… (Ctrl+S, defaults .mna), &Export Project as MNX… (Ctrl+Shift+E, always binary CBOR)
• Auto-save default path — default.xml → default.mna (auto-loaded on startup if present)
• Foreign-data preservation — round-trip saves preserve unknown fields via m_loadedMnaProject
• Modernised pipeline canvas — rounded-rect nodes with gradient fills, drop shadows, type labels (SENSOR / ALGORITHM), centred name, hollow-input / filled-output ports, Bezier connections with tangent arrowheads, dot-grid background, Tailwind-inspired palette, selection glow

MNE Browse

• Project reset on standalone open — opening a raw file without a project resets m_mnxProject to prevent stale-project contamination across all 5 file-open entry points (desktop menu, WASM picker, recent files, drag-drop, CLI)

WASM Progressive Web App

• PWA manifest + service worker — scripts/wasm/manifest.json, scripts/wasm/sw.js, 192×192 / 512×512 icons; offline caching with versioned cache keys; combined COOP/COEP header injection
• No server required — deploy bundle to any static host; service worker injects required headers for SharedArrayBuffer

Command-Line Tools

• Final MNE-C CLI parity (4 new): mne_make_movie (STC frames → PNG via FsSurface orthographic projection), mne_convert_lspcov (LISP S-expression covariance → FIFF FiffCov), mne_convert_ncov (ASCII ncov → FIFF), mne_dacq_annotator (event annotation replacing legacy Motif GUI)
• Inverse tools (7 new): mne_compute_cmne, mne_inverse_pipeline, mne_label_ssp, mne_average_estimates, mne_process_stc, mne_make_uniform_stc, mne_map_data
• Preprocessing tools (7 new): mne_add_triggers, mne_change_baselines, mne_change_nave, mne_copy_processing_history, mne_fix_stim14, mne_make_derivations, mne_toggle_skips
• Info tools (6 new): mne_check_eeg_locations, mne_evoked_data_summary, mne_list_coil_def, mne_list_proj, mne_sensor_locations, mne_show_mna
• Forward tools (3 new): mne_fit_sphere_to_surf, mne_make_scalp_surfaces, mne_transform_points
• Conversion tools (3 new): mne_convert_ctf_markers, mne_epochs2mat, mne_mna_bids_converter
• Total CLI inventory: 82 tools — full MNE-C feature parity

CI/CD

• Upgraded codecov/codecov-action from v5 to v6 to resolve Node.js 20 deprecation warnings
• Added MNE_REQUIRE_PYTHON: 'true' environment variable to all platform test steps
• Added scikit-learn to Python test dependencies
• Updated lodash from 4.17.23 to 4.18.1 (Dependabot security fix)

Bug Fixes

• Fixed potential silent test skips — Python-dependent tests now respect MNE_REQUIRE_PYTHON enforcement
• Fixed deprecated qWarn calls in test_mne_source_analysis (replaced with qWarning())
• Fixed unused [[nodiscard]] return values in test_tool_inverse_computation

Documentation

• Added 26 new command-line tool documentation pages
• Comprehensive MNA / MNX format manual page (mna-format.mdx, ~692 lines) — file types, BIDS-like data hierarchy, computational graph, execution modes, parameter system, op registry, verification & provenance, MNX byte layout, schema versioning, complete annotated JSON example
• Rewrote MNA API reference page (api-mna.mdx) with full class inventory (63 → 572 lines)
• Added ML library API reference page (api-ml.mdx)
• Added Statistics library API reference page (api-sts.mdx)
• Updated tools overview with all 26 new tools and new "Inspection and Information" section
• Updated overview and API pages with Mna, Ml, Sts library entries
• Expanded glossary with 14 new terms (CMNE, DICS, LCMV, MNA, MxNE, ONNX, etc.) and 3 file format entries (.mna, `...

ONNX Runtime Artifacts

Reusable ONNX Runtime shared library packages for CI and local development.

MNE-CPP v2.1.0

What's Changed

New Features

• MNE Browse overhaul

  • QRhi-based 2D channel rendering for Metal/Vulkan/D3D12 performance
  • ICA browser with component visualization, rejection, and original-data reset
  • Epoch review workflow with evoked computation and histogram view
  • Annotation workflow with FIF interoperability and auto-merge
  • Virtual channel derivations with weighted reference workflows
  • Covariance matrix heatmap visualization and whitening controls (W key)
  • Projector dialog (J/Shift+J) and SSP toggle
  • 2D layout view with mouse-wheel zoom, auto-scale, and channel scaling spinboxes
  • Dark mode, drag-and-drop file open, recent files list
  • GPU clipping/z-score shaders, fullscreen (F11), zen mode (F)
  • Linear detrending (D key cycles None/DC/Linear)
  • GFP overlay on butterfly view
  • Interactive ruler tool with amplitude snap and semi-transparent overlay
  • Double-click bad-channel marking, click-to-toggle bad channels
  • Stimulus lane above time ruler with event markers
  • Per-description event/annotation filtering and visibility toggles
  • Channel sort by type, epoch grid lines (G), overview bar toggle (O), scroll speed control
  • Source-estimate export workflow
  • Session filtering workflow
  • Settings persistence across sessions via QSettings
  • Event file saving to FIF and ASCII formats
  • WASM loading screen and optimized WebAssembly build

• MNE Analyze Studio

  • Agent-based workflow engine with grounded LLM safety
  • Multi-provider planner profiles (OpenAI Responses API)
  • Reusable inspect 3D surface views
  • Extension-based view architecture with hosted view tooling
  • VS Code chat UX integration and .mna project format

• BIDS library (mne_bids): New library for reading and writing BIDS-formatted datasets with testframe

• Beamformers: Added beamformer classes to the inv library with testframes

• DSP library enhancements

  • WelchPsd: Welch power spectral density estimation
  • MorletTfr: Morlet wavelet time-frequency representation
  • xDAWN: xDAWN spatial filtering for ERP denoising
  • KMeans: Cosine and correlation distance normalization implemented
  • Real-time covariance: Channel picks applied (MEG/EEG only)

• Logging: Renamed ApplicationLogger to MNELogger with MNE_LOG_LEVEL and MNE_LOG_MODE environment variables

CI/CD

• Qt 6.11 support with auto-detection in init.sh
• Build Qt Installer Framework 4.11.0 toolchains from source
• Offline self-contained installers (.run, .dmg, .exe)
• Nightly WASM builds deployed alongside stable releases
• Reusable Qt toolchain assets consumed by CI workflows
• Eigen downloaded at configure time (no longer bundled)

Bug Fixes

• Fixed Metal/QRhi rendering on macOS: native window, infinite repaint loop
• Fixed butterfly whitening scale and circular channel arrangement
• Fixed 2D layout channel filtering, scale persistence, and item sizing
• Fixed crosshair repaint cascade, split MEG grad/mag scale labels
• Fixed DSP SSS and bad-channel regressions
• Fixed DSP pi constants on Windows, params defaults on Clang/GCC
• Fixed Windows linker error for nested Params struct exports
• Fixed macOS test flakiness and WASM build errors
• Fixed mne_anonymize unique_ptr usage
• Fixed ruler amplitude precision (1 → 3 decimal places)
• Fixed stim chip overlap, event line z-order, and resize resampling
• Fixed scroll pan boundary and smooth inertial scroll

Documentation

• Updated website to reflect renamed/split libraries
• Updated build guide paths (tools/ → scripts/)
• Fixed release download page for installers and WebAssembly
• Updated Zenodo DOI to 19139238

Full Changelog: v2.0.0...v2.1.0

Eigen SDK Artifacts

Reusable Eigen CMake package bundles for CI and local development.

MNE-CPP v2.0.0

Versioning

• MNE-CPP libraries: Version 2.0.0
• CLI tools (51 ported MNE-C tools, mne_dipole_fit, mne_inspect): Derive version from the MNE-CPP project version (2.0.0) via CMake compile definition
• MNE Scan: Version 1.0.0 (first stable release as a standalone application)
• MNE Analyze: Version 1.0.0 (first stable release as a standalone application)
• IConnector plugin interface: Bumped to mne_rt_server/2.0

Breaking Changes

• Library renames: connectivity → conn, communication → com, rtprocessing → dsp, inverse → inv, disp3D_rhi → disp3D
• Class renames: Inverse library classes now use Inv prefix (InvRapMusic, InvMinimumNorm, InvSourceEstimate, InvHpiFit, …)
• Moved classes: InvInverseOperator, InvMeasData, InvMeasDataSet moved from inv to mne library (as MNEInverseOperator, MNEMeasData, MNEMeasDataSet); backward-compatible forwarding headers provided
• Moved classes: FwdForwardSolution moved to MNEForwardSolution in the mne library; forwarding header in fwd/ for backward compatibility
• Removed: InvCorSourceEstimate class (superseded by unified InvSourceEstimate)
• Split: MNEMath split into Linalg and Numerics in the math library
• Moved: events library moved into mne_analyze application (no longer a standalone library)
• Qt requirement: Qt 6.10.0 minimum (Qt 5 no longer supported)
• Eigen upgrade: Eigen 5.0.1

New Features

• 51 CLI tools: Ported all MNE-C command-line tools to modern C++ with QCommandLineParser and ApplicationLogger
  • Conversion: mne_edf2fiff, mne_ctf2fiff, mne_kit2fiff, mne_brain_vision2fiff, and more
  • Forward modeling: mne_forward_solution, mne_setup_forward_model, mne_prepare_bem_model, mne_make_source_space, mne_make_sphere_bem, mne_average_forward_solutions
  • Inverse: mne_compute_raw_inverse, mne_compute_mne, mne_inverse_operator
  • Preprocessing: mne_anonymize, mne_process_raw, mne_compensate_data
  • Surface: mne_surf2bem, mne_check_surface, mne_watershed_bem, mne_flash_bem
  • Info: mne_show_fiff, mne_compare_fif_files, mne_list_source_space, mne_list_bem
  • Server: mne_rt_server
  • Simulation: mne_simulate_data
• Unified InvSourceEstimate: Single class with composition layers for grid data, focal dipoles, couplings, connectivity, positions, and metadata; includes tokenization support for streaming
• RHI-based 3D rendering: Migrated from Qt3D to QRhi pipeline with holographic rendering mode, Fresnel effects, dipole overlay, and async STC loading
• Flexible clustering: Variable cluster sizes in source space computation
• MNE Scan improvements: Plugin loading progress on splash screen, macOS app bundle icons
• LSL library modernized: Added lsl_ prefix, comprehensive tests, updated to LSL 1.17.5

Refactoring & Modernization

• Forward library (fwd): Removed ~700 lines of dead code; replaced printf → qInfo/qWarning; replaced goto → early return/lambdas; replaced C macros (ARSINH, EPS) → constexpr/inline; modernized FwdBemModel members from raw pointers to Eigen types and std::shared_ptr
• FIFF I/O consolidation: Moved duplicated FIFF reading functions to library classes (FiffStream::read_bad_channels, MNECovMatrix::read, MNERawInfo::find_meas_info)
• Thread safety: Fixed thread-unsafe static float* in MNEProjOp::project_vector using thread_local
• Network input validation: Added bounds checking in BabyMEG client byte conversion functions
• Sparse matrix crash fix: Guarded MNEHemisphere::operator== against segfault on default-constructed sparse matrices
• Copyright: Updated to 2026 across all library headers
• Qt6 serialization: Updated QDataStream version from Qt_5_1 to Qt_6_0 in rt_server
• Centralized CLI versioning: All 51 CLI tools now derive their PROGRAM_VERSION from the CMake project version (MNE_CPP_VERSION) instead of hardcoded strings
• Format specifier fix: Fixed %d → %lld for qsizetype in BabyMEG client warnings

CI/CD

• Restructured to Main-Staging-Feature branch model
• Build matrix: Ubuntu 24.04, macOS 26, Windows 2025 with Qt 6.10.0 and Qt 6.10.2
• CodeQL and Coverity static analysis (weekly)
• Code coverage tracking with 35% library threshold
• CPackIFW-based installer generation (.run, .dmg, .exe)
• WebAssembly build support

Documentation

• Docusaurus-based documentation site
• Organized CLI tools by domain category in sidebar
• Added MNE handbook reference pages (cookbook, FIFF format, sample dataset, data conversion)
• Completed Doxygen documentation for InvRapMusic, InvMinimumNorm, InvDipole

Bug Fixes

• Fixed crash in make_inverse_operator with non-surface-oriented forward solutions
• Fixed segfault in forward computation
• Fixed FIFF double I/O, make_dir EOF, write_cov packing, and source_cov kind
• Fixed MNECTFCompDataSet copy constructor member initialization
• Fixed coordinate transformation handling in 3D visualization
• Fixed inflated brain alignment and surface projection tolerances
• Fixed floating-point comparison tolerances in forward solution tests
• Fixed sphere simplex test convergence

Qt Toolchain Artifacts

Reusable Qt runtime, static, WASM and Installer Framework assets for CI.

v0.1.9

For details please see the changelog for v0.1.9.