Version 1.13.0.dev197+ge1da4c068 (development) (2026-07-28)

Dependencies

• Updated minimum for:

  • Core dependency matplotlib >= 3.9

  Changes implemented via CI action created by Thomas Binns. (#13899)

• Updated minimum for:

  • Optional dependency scikit-learn >= 1.5

  Changes implemented via CI action created by Thomas Binns. (#13916)

• Switch the default Qt bindings from PyQt6 to PySide6. As a result, mne[full] now includes PySide6 instead of PyQt6. Users who prefer PyQt6 can continue to use mne[full-pyqt6], and mne[full-pyside6] remains available as an alias for mne[full]. Changes by Clemens Brunner. (#13960)

• PyQt5 is no longer an officially supported Qt binding, by Eric Larson. (#13981)

• Updated minimum for:

  • Core dependency numpy >= 2.0, < 3

  • Core dependency scipy >= 1.14

  Changes implemented via CI action created by Thomas Binns. (#14023)

• Updated minimum for:

  • Optional dependency pyvista >= 0.44

  Changes implemented via CI action created by Thomas Binns. (#14048)

• Raised minimum versions of some optional dependencies to comply with MNE-Python’s SPEC0-like policy, and added them to the set kept up to date automatically by the spec_zero CI job, by Eric Larson:

  • Optional dependency dipy >= 1.9

  • Optional dependency mne-qt-browser >= 0.6

  • Optional dependency nibabel >= 5.2

  • Optional dependency nilearn >= 0.10

  • Optional dependency numba >= 0.60 (#14108)

Bugfixes

• Fixed a bug in mne.stats.spatio_temporal_cluster_1samp_test() and related spatio-temporal permutation cluster functions where, in rare cases, clusters that should have been joined by a chain of spatial and temporal adjacency steps were incorrectly reported as separate clusters, by Sharif Haason. (#13731)

• Fix mode parameter in get_point_spread() and get_cross_talk() to correctly map public mode names ('max', 'svd') to internal names, expose previously hidden modes 'sum' and 'maxval' in the public API, and raise ValueError for invalid mode values, by new contributor Famous077. (#13754)

• Improved colocated OPM topomap handling by recognizing additional OPM coil types (FieldLine and Kernel), by Pragnya Khandelwal. (#13825)

• Fix bug where logging messages were sometimes errantly printed, by Eric Larson. (#13843)

• Fixed incorrect label orientation for nodes in the 0–90° polar range (the 12–3 o’clock quadrant) of the connectivity circle plot, by new contributor Pavel Popov. (#13855)

• Fixed an indexing bug in fNIRS support in mne.io.BaseRaw.interpolate_bads() (and related methods) that could errantly use incorrect donor channels, by new contributor Kalle Makela. (#13856)

• Add a memmap keyword argument to mne.io.BaseRaw.load_data(), allowing loading deferred raw data into a memory-mapped file after object creation, by Aniket Singh Yadav. (#13858)

• Completed triaxial OPM topomap grouping by rendering separate radial and tangential maps in plot_evoked_topomap() and plot_components(), and fixed shape-mismatch crashes in plot_projs_topomap() and animate_topomap() with colocated OPM channels, by Pragnya Khandelwal. (#13866)

• Fix handling of optional dependencies that don’t specify a version attribute, by new contributor Baris Talar. (#13870)

• Improved error message when FreeSurfer executable is not found, by new contributor Ayushi Satodiya. (#13874)

• Fix bug with mne.preprocessing.ICA.plot_properties() when using reject in mne.preprocessing.ICA.fit(), by Eric Larson. (#13885)

• Fix bug where picks was ignored in mne.Epochs.apply_function() when channel_wise=False, by Thomas Binns. (#13894)

• Fix iteration errors in mne.io.read_raw_nihon() when reading log files, by Tom Ma. (#13915)

• Fix bug with mne.set_eeg_reference() not working when passing a single channel name as string, by Michael Straube. (#13917)

• Fix mne.set_eeg_reference() so that passing a list of channel types with projection=False and ref_channels="average" now references each channel type independently by default (matching the projection=True path), by new contributor Ben Tang. Previously a single average was computed across the union of the listed types. Pass joint=True for the previous behavior. (#13920)

• Use mffpy-backed parsing for EGI MFF event tracks while tolerating nanosecond timestamps that some files store in beginTime, by Pragnya Khandelwal. (#13932)

• Fix mne.preprocessing.eyetracking.interpolate_blinks() so that all annotation descriptions passed via match are interpolated over, rather than only BAD_blink ones, by new contributor Vincent Gao. (#13940)

• Fix channel ordering bug in mne.viz.plot_compare_evokeds() when axes="topo", by Lifeng Qiu Lin. (#13943)

• Fix bug in mne.read_annotations() where reading a .txt file containing a single channel-specific annotation raised an AttributeError, by new contributor Piotr Durka. (#13962)

• Fixed bug where mne.sys_info() would silently change the active Matplotlib backend (e.g. when ipympl is installed) as an import-time side effect, by Stefan Appelhoff. (#13963)

• Fix bug where mne.preprocessing.write_fine_calibration() wrote internal MEG channel names (e.g. MEG0113) instead of the bare channel numbers (e.g. 113) that MaxFilter expects, breaking round trips of Neuromag calibration files, by new contributor Apoorva Verma. (#13999)

• Fix mne.preprocessing.eyetracking.read_eyelink_calibration() to decode .asc files as UTF-8 instead of ASCII, so non-ASCII characters in MSG lines no longer raise a UnicodeDecodeError, by new contributor Cedric Conday. (#14002)

• Fix the error message raised when a requested FIR filter_length is too short, which reported half the actual transition bandwidth, by Cedric Conday. (#14005)

• Fixed several error messages that displayed literal {...} placeholder text instead of the intended values, due to a missing f string prefix (in mne.SourceEstimate, mne.io.read_raw_hitachi(), mne.preprocessing.compute_current_source_density(), and mne.preprocessing.maxwell_filter()), by Cedric Conday. (#14008)

• Fix bug where mne.concatenate_epochs() could silently concatenate epochs with conflicting event_id dicts, by Eric Larson. (#14051)

• Fixed two bugs in how SSS information is stored and read: mne.preprocessing.maxwell_filter() recorded which multipole moments it had kept in the wrong order (the filtered data itself was unaffected), and mne.compute_rank() reported the full MEG rank rather than the reduced SSS rank for data processed with MaxFilter™-3.0, by Eric Larson. (#14059)

• Fix figures not being displayed in notebook-style frontends when using a Matplotlib inline backend, by Mingjian He. (#14076)

• Fix Qt browser close messages from mne.io.Raw.plot() appearing in the wrong Jupyter notebook cell, by Mingjian He. (#14077)

• When concatenating Raw objects containing annotations, also merge the extras fields, by Marijn van Vliet (#14084)

• Fixed plot_evoked_topomap() and plot_sensors() (and the plot_sensors methods) to follow Matplotlib’s blocking behavior when show=True instead of returning immediately; plot_sensors keeps its block argument (default now None), by Clemens Brunner. (#14098)

• Fixed bug in mne.io.Raw.plot() where, with the matplotlib backend and group_by="selection", the channel-selection radio buttons no longer all appeared selected while in butterfly mode, by Eric Larson. (#14108)

API changes by deprecation

• Rename standard_1005 and standard_1020 montages to colin27_1005 and colin27_1020, respectively. If you used standard_1005 or standard_1020, either switch to the new names colin27_1005 and colin27_1020 or use the new spherical montages spherical_1005, spherical_1010, or spherical_1020, which provide idealized template locations on a sphere (useful for plotting). By Clemens Brunner. (#13903)

• In mne.Evoked.animate_topomap() the vmin and vmax keyword arguments have been deprecated in favor of vlim, by Eric Larson. (#13905)

• In mne.viz.iter_topography(), the on_pick callable for sub-figures now has a new parameter orig_fig that refers to the main figure. To preserve backward compatibility, it is made optional. By Lifeng Qiu Lin. (#13968)

• The block parameter of mne.time_frequency.Spectrum.plot_topo(), the legacy plot_psd_topo methods, and mne.viz.plot_raw_psd_topo is deprecated and will be removed in MNE 1.15; these plots now follow Matplotlib’s blocking behavior, by Clemens Brunner. (#14098)

New features

• Add mne.preprocessing.eyetracking.find_blinks() to detect blinks in eye-tracking data from pupil dropouts and return them as Annotations, by Stefan Appelhoff. (#12946)

• It is now possible to concatenate raw objects with mne.concatenate_raws() as long as they inherit from BaseRaw, even if their specific types differ (e.g., Raw and RawArray), by Clemens Brunner. (#13263)

• Add a preprocessing example showing how to explore epoch quality before rejection using robust statistics (peak-to-peak amplitude, variance, and kurtosis) inspired by FASTER (Nolan et al., 2010) and Delorme et al. (2007), by Aman Srivastava. (#13710)

• Speed up mne.stats.spatio_temporal_cluster_1samp_test() and related permutation cluster functions via precomputed sum-of-squares for sign-flip t-tests and SciPy connected-components clustering (~5x), by new contributor Sharif Haason. (#13731)

• Add annotation_colors parameter to mne.io.Raw.plot() and mne.Epochs.plot() to allow users to specify custom colors for annotations by passing a dict mapping annotation description strings to colors (for example, annotation_colors=dict(bad_segment="orange")), by Clemens Brunner. (#13838)

• Add dark theme support (theme="light", "dark", or "auto") to the 'matplotlib' browser backend used by mne.io.Raw.plot(), mne.Epochs.plot(), and mne.preprocessing.ICA.plot_sources(), by Clemens Brunner. (#13861)

• Fix mne.preprocessing.nirs.beer_lambert_law() to support explicitly provided sd_distances during Beer-Lambert conversion. When valid source-detector distances are already present in raw.info, overriding them now emits a warning, and when all inferred distances are invalid and no explicit distances are provided, a ValueError is raised instead of silently producing zero concentrations, by new contributor Kalle Makela. (#13875)

• Add overrides parameter to mne.io.read_raw_brainvision() for reading non-spec-compliant .vhdr files where the header contradicts the actual layout (e.g. renamed BIDS siblings, missing MarkerFile=, truncated [Channel Infos]). Accepts a dict with keys data_fname, marker_fname, n_channels, sfreq, ch_names, units_fallback, data_orientation, data_format, and binary_format; see the function docstring for details. Missing or empty MarkerFile= is now also tolerated natively (per the BV Core Data Format spec). When MarkerFile= names a path that does not exist (common after BIDS renames), mne.io.read_raw_brainvision() now falls back to the co-located <stem>.vmrk next to the .vhdr and warns, instead of raising FileNotFoundError, by Bruno Aristimunha. (#13884)

• Add idealized spherical 10–05, 10–10, and 10–20 montages (spherical_1005, spherical_1010, spherical_1020), by Clemens Brunner. (#13903)

• Improved mne.Report by:

  • Using "agg" backend for 2D plots to avoid windows unnecessarily popping up

  • Improving add_stc() by using direct capture of brain images, allowing direct control of image size using stc_plot_kwargs["size"]

  • Improving add_evokeds() evoked topomap plotting by using mne.Evoked.animate_topomap() with butterfly=True rather than re-plotting each topomap in a loop

  Also improved mne.Evoked.animate_topomap() by deduplicating code with mne.Evoked.plot_topomap(). Changes by Eric Larson. (#13905)

• Add support for reading cross-talk and fine-calibration embedded in FIF files during acquisition into raw.info["cross_talk"] and raw.info["fine_calibration"], respectively, by Eric Larson. (#13911)

• Add support for interactive label browsing using hover=True in mne.viz.Brain.add_annotation(), by Eric Larson. (#13931)

• Added 'fsaverage_1005' montage, which is a slightly improved version of the existing 'colin27_1005' montage (known in 1.12 and older as 'standard_1005'). The electrodes have already been mapped to the fsaverage head surface. Changes by Eric Larson. (#13936)

• Added basic support for TD fNIRS data, by new contributor Zahra Aghajan, new contributor Julien Dubois, new contributor John Griffiths, Robert Luke, and Eric Larson. (#13938)

• Add support for automatic cross_talk and fine_calibration adjustments in mne.preprocessing.maxwell_filter() when these are stored in mne.Info during acquisition (e.g., by newer MEGIN acquisition software), by Eric Larson. (#13942)

• Added the n_components parameter to ICA plotting and report generation functions to allow dynamic control over the number of components displayed by Athish M. (#13958)

• Added a volume_options["interpolation"] option to mne.viz.plot_source_estimates() and mne.viz.Brain.add_data() to control the interpolation method used for volume rendering. It can be "linear" (default) or "nearest". Changes by Eric Larson. (#13966)

• Include label and description fields when reading EGI mff files, by Martin Oberg. (#13967)

• Add TimeChange behaviour for mne.viz.plot_evoked_topo(), where time is marked with solid vertical line after clicking on subfigure axis. Add recursive parameter to mne.viz.ui_events.link() that enables linking to a target figure, as well as all figures that the target figure links to, by Lifeng Qiu Lin. (#13968)

• Add mask_label_params parameter to plot_topomap() and plot_evoked_topomap() to allow for customisation of masked channel labels, by Carina Forster. (#13969)

• Added public mne.viz.LayeredMesh class (previously private _LayeredMesh) with a smooth_mat attribute for efficient real-time source-space data streaming. Added Brain.layered_meshes attribute to access meshes after plotting, and a key parameter to mne.viz.Brain.add_data() for named overlays, by new contributor Payam Sadeghi-Shabestari. (#13970)

• Skip replotting of annotations on the horizontal scrollbar in the matplotlib browser backend, resulting in a significant speedup for traces with a large number of annotations by Frankie Robertson. (#13972)

• Allow subclasses of MNEBrowseFigure to be passed to plot_raw/plot_epochs, as well as the corresponding plot(...) methods of the raw and epochs classes, by new contributor Frankie Robertson (#13979)

• Add mouse wheel scrolling support to the 'matplotlib' browser backend to navigate through channels, by Clemens Brunner. (#13988)

• add_data() now supports multiple simultaneous overlays via remove_existing=False and distinct key values. The remove_existing parameter now accepts True / False in addition to None. By Payam Sadeghi-Shabestari. (#13995)

• Add on_outside parameter to mne.Epochs and mne.EpochsArray classes to control the behaviour when events exist outside the data range. The options are to 'warn' (new default), 'raise', or 'ignore' (old behaviour), by Cedric Conday. (#14004)

• mne.viz.Brain’s silhouette option now accepts a spacing string (e.g. "ico5", now the default) to decimate using the same vertex-picking as mne.setup_source_space() instead of a generic mesh decimation. mne.viz.plot_alignment() and mne.viz.Brain should also be faster when plotting many sensors (e.g., whole-head MEG systems), by Eric Larson. (#14016)

• Add a show_zero_line parameter (and 0 keyboard shortcut) to mne.io.Raw.plot() and mne.Epochs.plot() to show a reference line at each channel’s zero, by Clemens Brunner. (#14018)

• Make mne.viz.plot_evoked_topo() show the currently select time with a solid vertical line also in the main figure, by Marijn van Vliet. (#14032)

• Added a weighted option to mne.chpi.compute_head_pos() that fits all cHPI coils simultaneously with per-coil weights derived from their goodness of fit and inter-coil distance error, avoiding discontinuous jumps (“teleporting”) in the estimated head position caused by coils switching in and out of the best-three subset (#11330). The default will change from False to True in version 1.14; until then, leaving it unset emits a FutureWarning. By Eric Larson. (#14034)

• More complete type checking has been implemented for mne.io, plus Epochs and Evoked, by Eric Larson. (#14036)

• When multiple overlays are active (via remove_existing=False in add_data()), the interactive Brain viewer now shows an “Overlay” drop-down in the Color Limits dock panel that lets the user switch which overlay’s color limits and smoothing the sliders control. By Payam Sadeghi-Shabestari. (#14037)

• Make the vertical (channel) and horizontal (time) scrollbar handles in the 'matplotlib' browser backend draggable, by Clemens Brunner. (#14040)

• The colorbar in the mne.viz.Brain viewer now automatically switches to scientific notation for tick labels, and has more tick-label spacing. The Help dialog now uses a Qt dialog styled to match mne-qt-browser’s help dialog instead of a matplotlib popup, and the “Press ? for help” status bar message is now clickable, and “Help” text was removed from the top left of the GUI by Payam Sadeghi-Shabestari. (#14054)

• Added support for newer recording software in mne.io.read_raw_nirx(), by Emma Bailey. (#14055)

• Added type annotations to public members of mne/io, mne.Evoked, and mne.Epochs, by Eric Larson. (#14056)

• Sped up mne.stats.spatio_temporal_cluster_1samp_test() by graph reduction and more efficiently applying sign-flips, by Eric Larson. (#14057)

• mne.viz.plot_ica_components() and mne.preprocessing.ICA.plot_components() now set the window title to “Independent Components” instead of adding a suptitle and append the plotted component range when it is contiguous, by Clemens Brunner. (#14058)

• Added regularize="in_argmax" to mne.preprocessing.maxwell_filter() to allow component selection more similar to that of MaxFilter™-2.2, by Eric Larson. (#14059)

• Speed up and slightly improved the accuracy of mne.make_forward_solution(), by Eric Larson. (#14061)

• The colorbar in the mne.viz.Brain viewer now shows tick marks aligned with its labels, and its title now defaults to the active overlay’s key (see add_data()). The interactive viewer can show vertex coordinates and camera orientation, toggled via the v key or a new toolbar button, by Payam Sadeghi-Shabestari. (#14062)

• On Linux, mne.sys_info() now includes the detected windowing system (Wayland or X11), by Clemens Brunner. (#14099)

Other changes

• Adopting the diataxis framework by improving the phantom dipole tutorial, by Carina Forster. (#13584)

• Reorganized EDF submodule structure by moving private functionality into the public mne.io namespace to improve module consistency and avoid exposing private modules in the Credits page, by Aniket Singh Yadav. (#13673)

• Document onset, duration, description, and ch_names attributes of mne.Annotations, by Famous077. (#13680)

• Remove numpy.ndarray from colormap parameter in mne.viz.plot_source_estimates() to solve documentation conflict , by new contributor Lifeng Qiu Lin. (#13797)

• Added cross-references to common modification methods in mne.Info docstring by new contributor Athish M. (#13811)

• Adding checks in mne.stats.permutation_t_test() to warn the user when provided with bad input values, by Himanshu Mahor. (#13813)

• Added regression coverage for colocated triaxial OPM topomap handling in plot_joint() and ICA.plot_components(), by Pragnya Khandelwal. (#13842)

• Add notes to set_eeg_reference() and Setting the EEG reference about the correct procedure to create an average reference, by new contributor Deep Kaur and new contributor Farzah11. (#13846)

• Added a helper to split colocated OPM overlap sets into radial and tangential channel groups, and updated topomap regression coverage to use shared triaxial OPM fixtures, by Pragnya Khandelwal. (#13847)

• Fixed typos in error messages when reading measurement info, by new contributor Seth Bashford. (#13881)

• Fixed the fun shape description in mne.Epochs.apply_function()’s docstring, by new contributor Bhargav Kowshik. (#13891)

• Batch and vectorise classifier estimation and scoring in mne.decoding.GeneralizingEstimator.score() for scoring=None, "accuracy", "balanced_accuracy" and "roc_auc", by new contributor Mathias Sablé-Meyer. (#13909)

• Convert non-empty drop_log entries from numpy.str_ to regular Python strings, by Clemens Brunner. (#13923)

• Refactor the EGI MFF reader to use mffpy for metadata parsing, improving robustness and maintainability. This includes a shim for PNS sensor parsing to bypass an upstream bug in mffpy and resolves channel naming inconsistencies, by Pragnya Khandelwal. (#13945)

• Replace the internal binary-block EEG sample reader in mne.io.read_raw_egi() with mffpy-backed reading via mffpy.Reader.get_physical_samples_from_epoch, removing manual block-header parsing and np.fromfile calls, by Pragnya Khandelwal. (#13973)

• Converted the remaining percent-style string formatting to f-strings in internal code, by new contributor Théo Castillo. (#13974)

• Replace defusedxml-backed implementations of _get_ep_info and _get_signalfname in the EGI MFF reader with mffpy-backed parsing via mne.io.read_raw_egi(), by Pragnya Khandelwal. (#13991)

• Replace defusedxml-backed _get_gains with mffpy-backed parsing via mne.io.read_raw_egi() and remove the internal _extract helper, fully eliminating defusedxml from the EGI MFF reader, by Pragnya Khandelwal. (#14007)

• Add table with all available config options to Configuring MNE-Python, by Clemens Brunner. (#14010)

• Remove _get_eeg_calibration_info from the EGI MFF reader and delegate per-channel GCAL scaling to mffpy’s native calibration, simplifying EEG channel calibration in mne.io.read_raw_egi(), by Pragnya Khandelwal. (#14011)

• Replace the manual PNS binary block reader in mne.io.read_raw_egi() with mffpy-backed reading via get_physical_samples_from_epoch, by Pragnya Khandelwal. (#14030)

• Replace manual binary block reader _get_blocks with mffpy.Reader API in _read_mff_header, removing low-level EGI binary parsing in favour of the existing mffpy dependency, by Pragnya Khandelwal. (#14043)

• Remove dead placeholder keys gain, bits, and value_range from _read_header in egimff.py; these were hardcoded to zero and unused since MFF calibration is handled via CAL_SCALES, by Pragnya Khandelwal. (#14047)

• Document how to check and tune the OpenBLAS thread count when decomposition-heavy operations are unexpectedly slow, by new contributor Daria Agafonova. (#14064)