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Improvements 3d renderer#1102

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ElpadoCan wants to merge 15 commits into
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improvements_3d_renderer
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Improvements 3d renderer#1102
ElpadoCan wants to merge 15 commits into
mainfrom
improvements_3d_renderer

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@ElpadoCan

@ElpadoCan ElpadoCan commented May 19, 2026

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This PR implements UI improvements and Cell ID selector for the 3D renderer (see #1096)

keejkrej and others added 8 commits May 6, 2026 21:40
@keejkrej @claude
feat: add GPU-accelerated 3D z-stack renderer
a3ad90e 
Implements a standalone vispy-based 3D volume renderer with full Cell_ACDC
integration: multi-channel overlay, segmentation mask volumes, anisotropic
voxel scaling, plane/ISO/MIP depiction modes, smooth-ISO pre-filter,
percentile auto-contrast, opacity/contrast controls, keyboard shortcuts,
QSettings persistence, and screenshot export.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@ElpadoCan
fix: install vispy and PyOpenGL for CI tests
6e9efa5
@ElpadoCan
fix: test_rendered3d failing
0f64a81
@ElpadoCan
fix: test_rendered3d failing because of GUI init
3f0d6f2
@ElpadoCan
fix: test_rendered3d failing because not closing gui elements
ca5f179
@ElpadoCan
ci: ignore test_renderer3d because it requires a GUI environment
5fdb923
@ElpadoCan
WIP: improving UI of 3D renderer
537cd96
@ElpadoCan
improvement: use launch 3d renderer button with 3d icon
1dd00e8
@ElpadoCan

ElpadoCan commented May 20, 2026 •
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To implement:

  • "Clim:" as the same colorbar slider we already have in the main GUI
  • Include the Auto and Full buttons for the LUT slider
  • Colormap from the LUT slider
  • Gamma correction as a slider with numeric control
  • Step as a slider with numeric control
  • Opacity as a grayscale colorbar slider on the right side
  • "View" button as a button with a home icon in toolbar
  • Top toolbar with "Home" and "Save" buttons
  • Shortcut H for home button
  • Overlaid segmentation masks
  • Overlaid fluorescence channels
  • Opacity sliders for overlaid channels
  • LUT slider for additional channels
  • Opacity slider for overlaid segmentation masks
  • Cell ID selector to show only that cell
  • Clickable Cell ID to show only that cell
  • z-anisotropy correction factor with the function scipy.ndimage.zoom
  • z-anisotropy correction factor as a numeric control

@ElpadoCan ElpadoCan mentioned this pull request May 25, 2026
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@ElpadoCan ElpadoCan mentioned this pull request Jun 15, 2026
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@ElpadoCan

ElpadoCan commented Jun 15, 2026

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Closing this because development of this feature continues in PR #1120

@ElpadoCan ElpadoCan closed this Jun 15, 2026
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@ElpadoCan @keejkrej