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Add alpha transparency parameter to 3D heatmaps - #115

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AdityaGupta716 wants to merge 3 commits into
brainglobe:mainfrom
AdityaGupta716:feature/alpha-transparency-3d-heatmap
Open

Add alpha transparency parameter to 3D heatmaps#115
AdityaGupta716 wants to merge 3 commits into
brainglobe:mainfrom
AdityaGupta716:feature/alpha-transparency-3d-heatmap

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@AdityaGupta716

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Closes #101

Summary

Adds an alpha parameter to Heatmap.__init__() so users can control
brain region transparency in 3D format directly, without manually
accessing brainrender actors.

Usage

Global alpha (all regions):

bgh.Heatmap(values, ..., format="3D", alpha=0.5)

Per-region alpha:

bgh.Heatmap(values, ..., format="3D", alpha={"HIP": 0.3, "TH": 0.8})

Changes

  • brainglobe_heatmap/heatmaps.py — new alpha parameter with validation
  • tests/test_unit/test_alpha.py — unit and integration tests
  • examples/heatmap_3d_alpha.py — new example

Notes

  • None by default — fully backwards compatible
  • Has no effect in 2D format
  • Values validated at init time with clear error messages

@codecov

codecov Bot commented Mar 2, 2026

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Codecov Report

❌ Patch coverage is 53.33333% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 68.91%. Comparing base (0fea8e1) to head (54830a1).

Files with missing lines Patch % Lines
brainglobe_heatmap/heatmaps.py 53.33% 7 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #115      +/-   ##
==========================================
- Coverage   69.63%   68.91%   -0.72%     
==========================================
  Files           5        5              
  Lines         326      341      +15     
==========================================
+ Hits          227      235       +8     
- Misses         99      106       +7     

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@AdityaGupta716
AdityaGupta716 force-pushed the feature/alpha-transparency-3d-heatmap branch 2 times, most recently from 65ec89e to e6ef82a Compare March 2, 2026 21:33
@AdityaGupta716
AdityaGupta716 force-pushed the feature/alpha-transparency-3d-heatmap branch from 98fc4ff to f52760a Compare March 2, 2026 22:06
@AdityaGupta716

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hi @adamltyson plz review whenever ur free , let me know if there are any changes u would like !

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Allow user to set transparency of region in 3D heatmaps

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