ENH: support per-vertex opacity in 3D overlays by PragnyaKhandelwal · Pull Request #13706 · mne-tools/mne-python

PragnyaKhandelwal · 2026-02-28T19:23:00Z

Reference issue
Fixes #13679

What does this implement/fix?
This PR adds support for per-vertex opacity in 3D distributed source overlays.

Previously, overlay opacity was effectively handled as a scalar value. This change allows opacity to be either:

a scalar (existing behavior), or
a 1D array with one value per vertex ([shape (n_vertices,)]
Implementation details:

Keeps the existing per-vertex RGBA pipeline and lets VTK handle triangle interpolation.
Adds explicit validation and clear error messages for invalid opacity shapes.
Updates related documentation for overlay alpha behavior.
Adds tests for:
valid per-vertex opacity usage, and
invalid-shape opacity failure cases.

Additional information
The branch is clean and focused on this issue.
No extra/demo files are included in the PR.
Targeted tests and pre-commit checks for modified files pass locally.

…lwal/mne-python into enh-vertex-opacity

wmvanvliet

Could we modify one of the examples, or add a new one, to show off this functionality?

Code looks good!

Co-authored-by: Eric Larson <[email protected]>

…ploader" This reverts commit 67ea126.

PragnyaKhandelwal · 2026-03-05T07:36:55Z

All checks are now green. I have applied the suggested .. versionchanged:: tag, reverted the Codecov CI changes as requested, and added the example for Brain per-vertex opacity. Ready for a final look and merge when you have a moment!

larsoner

Pushed a tiny tweak to the example, marking for merge-when-green, thanks @PragnyaKhandelwal !

welcome · 2026-03-05T16:21:36Z

🎉 Congrats on merging your first pull request! 🥳 Looking forward to seeing more from you in the future! 💪

PragnyaKhandelwal · 2026-03-05T16:24:10Z

Thank you, @larsoner! I’m very grateful for the detailed reviews and the opportunity to collaborate with the team on this.

I've learned a lot through this process and am looking forward to getting my other pending PRs across the finish line and contributing more to MNE-Python in the future!

drammock · 2026-03-05T16:31:45Z

ping @jstout211: this feature is now live on main

PragnyaKhandelwal · 2026-03-06T08:29:43Z

Hi @jstout211,

Per @drammock's note in the original issue, I wanted to let you know that the support for per-vertex opacity in 3D overlays is now live on main via PR #13706.

This should allow for the distributed source visualization you were looking for. If you have any feedback while testing it out, feel free to share!

jstout211 · 2026-03-06T15:48:03Z

Hi @jstout211,

Per @drammock's note in the original issue, I wanted to let you know that the support for per-vertex opacity in 3D overlays is now live on main via PR #13706.

This should allow for the distributed source visualization you were looking for. If you have any feedback while testing it out, feel free to share!

Thanks to everyone for working on this. Appreciate the quick turnaround on this feature request.

Co-authored-by: Eric Larson <[email protected]>

* [pre-commit.ci] pre-commit autoupdate (mne-tools#13646) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Fix and extend anonymize_info (mne-tools#13647) * Fix epochs.plot() scrollbar issue (mne-tools#13654) * ENH: Add optional channel name overlay to plot_alignment (mne-tools#13570) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * Fix docstrings for get_data() (mne-tools#13652) * DOC: Add detail to make_watershed_bem volume parameter (mne-tools#13658) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13663) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * update maintainers lists (mne-tools#13631) * Fixes make_scalp_surfaces (mne-tools#13024) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Marijn van Vliet <[email protected]> Co-authored-by: Eric Larson <[email protected]> * DOC: Add pybvrf [skip azp] [skip actions] (mne-tools#13665) * Expose bem submodule (mne-tools#13669) * Rename `Epochs.reset_drop_log_selection()` to `Epochs.reset_index()` (mne-tools#13675) * MAINT: Work around NumPy deprecation (mne-tools#13677) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13678) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Allow reading alternative nasion label (Nz) from snirf file (mne-tools#13672) Co-authored-by: Daniel McCloy <[email protected]> * use a lockfile for "old" CI job (mne-tools#13490) Co-authored-by: Carina Forster <[email protected]> Co-authored-by: Thomas S. 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Binns <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> * ENH: support per-vertex opacity in 3D overlays (mne-tools#13706) Co-authored-by: Eric Larson <[email protected]> * FIX: Spelling [ci skip] * Fix generation of lockfile for old job (mne-tools#13724) * eyetrack should not count as picks=data (mne-tools#13723) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Scott Huberty <[email protected]> * BUG: prevent NaNs in layered overlay compositing when resulting alpha is zero (mne-tools#13714) Co-authored-by: Marijn van Vliet <[email protected]> * Added HEDAnnotations (mne-tools#13059) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Bru <[email protected]> Co-authored-by: Stefan Appelhoff <[email protected]> * [dependabot]: Bump the actions group with 2 updates (mne-tools#13728) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13734) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * Raising meaningful warnings/errors for interpolate_bads, when supplie… (mne-tools#13518) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * BUG: Fix bug with default (mne-tools#13744) * DOC: document first_samp behavior after crop and RawArray workaround (mne-tools#13685) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * FIX: do not print dev_head_t if not available (mne-tools#13741) Co-authored-by: Eric Larson <[email protected]> * FIX: Link [ci skip] * Update name [ci skip] * MAINT: cleanup Python 3.9 compat from __future__ import annotations (mne-tools#13749) Co-authored-by: Marijn van Vliet <[email protected]> * FIX: Handle hidden annotations during deletion in mpl plot (mne-tools#13703) * ENH: Log scaling better (mne-tools#13758) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13762) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * FORWARD: assert invariant for unreachable rref branch in _lead_dots (mne-tools#13764) * Improve handling of dropped epochs in ica.plot_properties (mne-tools#13746) * Support mixed hed annotations, concat and solve version registration (mne-tools#13736) * ENH: compute CSD directly for upper-triangle channel pairs in Fourier/multitaper (mne-tools#13719) * Extend plot_csd support to SEEG, ECoG, and DBS channel types (mne-tools#13713) Co-authored-by: Thomas S. 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(mne-tools#13813) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Erica R Peterson <[email protected]> * MAINT: Update dependency specifiers (mne-tools#13899) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * [dependabot]: Bump github/codeql-action from 4.35.3 to 4.35.4 in the actions group (mne-tools#13901) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13902) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Remove workaround for old PySide6 (mne-tools#13900) * Add spherical montages (mne-tools#13903) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13918) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13919) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Update dependency specifiers (mne-tools#13916) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * BUG: set_eeg_reference list ch_type now applies per-type CAR by default (mne-tools#13920) * FIX: Avoid iteration errors caused by None when reading Nihon Kohden .LOG files (mne-tools#13915) * Fix drop_log dtype (mne-tools#13923) * Doc: add guidance on taking over a stale pull request (mne-tools#13877) Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> * FIX: Make set_eeg_reference working with a string for a channel name (mne-tools#13917) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Clemens Brunner <[email protected]> Co-authored-by: Aman Srivastava <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Himanshu Mahor <[email protected]> Co-authored-by: Scott Huberty <[email protected]> Co-authored-by: Victor Férat <[email protected]> Co-authored-by: Marijn van Vliet <[email protected]> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: Aniket <[email protected]> Co-authored-by: Carina Forster <[email protected]> Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Erica Peterson <[email protected]> Co-authored-by: Horizon_Architect_07 <[email protected]> Co-authored-by: Pragnya <[email protected]> Co-authored-by: Benedikt Ehinger <[email protected]> Co-authored-by: Kay Robbins <[email protected]> Co-authored-by: Bru <[email protected]> Co-authored-by: Stefan Appelhoff <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Johannes Herforth <[email protected]> Co-authored-by: Hansuja <[email protected]> Co-authored-by: Simon Kern <[email protected]> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Akhilesh <[email protected]> Co-authored-by: CHH <[email protected]> Co-authored-by: Teon L Brooks <[email protected]> Co-authored-by: Lifeng <[email protected]> Co-authored-by: Kalle Mäkelä <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Pavel Popov <[email protected]> Co-authored-by: Ayushi Satodiya <[email protected]> Co-authored-by: Seth Bashford <[email protected]> Co-authored-by: Baris <[email protected]> Co-authored-by: Claude Sonnet 4.6 <[email protected]> Co-authored-by: Jonas Mago <[email protected]> Co-authored-by: Bhargav Kowshik <[email protected]> Co-authored-by: Erica R Peterson <[email protected]> Co-authored-by: Ben Tang <[email protected]> Co-authored-by: myd7349 <[email protected]> Co-authored-by: Michael Straube <[email protected]>

PragnyaKhandelwal added 3 commits February 27, 2026 14:16

ENH: support per-vertex opacity in 3D overlays

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ENH: support per-vertex opacity in 3D overlays

8df7208

Merge branch 'enh-vertex-opacity' of https://github.com/PragnyaKhande…

532490b

…lwal/mne-python into enh-vertex-opacity

PragnyaKhandelwal requested review from drammock, larsoner and wmvanvliet as code owners February 28, 2026 19:23

PragnyaKhandelwal mentioned this pull request Feb 28, 2026

set opacity per-vertex #13679

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wmvanvliet reviewed Feb 28, 2026

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PragnyaKhandelwal marked this pull request as draft March 1, 2026 07:08

PragnyaKhandelwal marked this pull request as ready for review March 1, 2026 07:51

DOC: add Brain example for per-vertex opacity

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PragnyaKhandelwal requested a review from agramfort as a code owner March 1, 2026 07:55

PragnyaKhandelwal requested a review from wmvanvliet March 1, 2026 08:06

PragnyaKhandelwal marked this pull request as draft March 1, 2026 08:13

PragnyaKhandelwal added 2 commits March 1, 2026 15:37

DOC: fixed CI doc warning

959b527

Fix CI: update contributor link, changelog ref, and Codecov uploader

67ea126

PragnyaKhandelwal marked this pull request as ready for review March 1, 2026 19:07

CI: add ver-auto-bumped extra

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larsoner reviewed Mar 2, 2026

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Comment thread mne/viz/_brain/_brain.py

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Comment thread azure-pipelines.yml Outdated

PragnyaKhandelwal and others added 4 commits March 2, 2026 22:36

Apply suggestion from @larsoner

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Co-authored-by: Eric Larson <[email protected]>

Revert "Fix CI: update contributor link, changelog ref, and Codecov u…

7d9b1f6

…ploader" This reverts commit 67ea126.

Merge branch 'main' into enh-vertex-opacity

ef57247

Merge branch 'mne-tools:main' into enh-vertex-opacity

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PragnyaKhandelwal requested a review from larsoner March 5, 2026 07:33

wmvanvliet approved these changes Mar 5, 2026

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Merge branch 'main' into enh-vertex-opacity

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larsoner approved these changes Mar 5, 2026

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FIX: Tweak example

21697a2

FIX: Cruft

6c259f6

larsoner enabled auto-merge (squash) March 5, 2026 14:55

larsoner merged commit 0de3a35 into mne-tools:main Mar 5, 2026
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sseth pushed a commit to xannnimal/mne-python that referenced this pull request Mar 25, 2026

ENH: support per-vertex opacity in 3D overlays (mne-tools#13706)

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Co-authored-by: Eric Larson <[email protected]>

PragnyaKhandelwal mentioned this pull request Apr 10, 2026

towncrier snafu on multiline changelog entry #13828

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ENH: support per-vertex opacity in 3D overlays - #13706

ENH: support per-vertex opacity in 3D overlays#13706
larsoner merged 14 commits into
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PragnyaKhandelwal:enh-vertex-opacity

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PragnyaKhandelwal commented Feb 28, 2026 •

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