Skip to content

Improvements 3d renderer#1102

Draft
ElpadoCan wants to merge 11 commits into
mainfrom
improvements_3d_renderer
Draft

Improvements 3d renderer#1102
ElpadoCan wants to merge 11 commits into
mainfrom
improvements_3d_renderer

Conversation

@ElpadoCan
Copy link
Copy Markdown
Collaborator

@ElpadoCan ElpadoCan commented May 19, 2026

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
Copy link
Copy Markdown
Collaborator Author

ElpadoCan commented May 20, 2026 •
edited
Loading

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@ElpadoCan @keejkrej