Volume Renderer v2 by ElpadoCan · Pull Request #1120 · SchmollerLab/Cell_ACDC

ElpadoCan · 2026-06-15T07:59:49Z

Taking inspiration from PRs #1110, #1102, #1096, #1106, and from https://github.com/keejkrej/acdc-son, this PR implements a 3D volume renderer that can be launched from a Python script (see below), or from the module 3 GUI.

Minimal code:

renderer = VolumeRendererWindow()
renderer.set_volume(zstack_array)   # (Z, Y, X) numpy array
renderer.run()

Features:

…_ACDC into renderer_3d_v2

Copilot

Pull request overview

This PR introduces a new VisPy-based 3D volume rendering window (VolumeRendererWindow) with multi-channel LUT/opacity controls, segmentation-mask overlay, and optional points layers, and integrates it into the main Cell-ACDC GUI via a “Launch 3D viewer” action/button.

Changes:

Added a new 3D volume-renderer module (canvas + toolbar widgets) with blending utilities and voxel scaling helpers.
Extended colormap/gradient and points-layer UI infrastructure (PyQtGraph↔VisPy symbol mapping, gradient shuffle actions, points appearance dialog support).
Wired the renderer into the GUI and added demo scripts + data downloader for quick testing.

Reviewed changes

Copilot reviewed 21 out of 22 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
`cellacdc/widgets.py`	Adds VisPy marker symbol combobox, gradient widget refactor, LUT state helpers, and context-menu plumbing used by the 3D renderer.
`cellacdc/volume_renderer/utils.py`	Adds voxel-size→display scaling helper for (Z,Y,X) data.
`cellacdc/volume_renderer/gl_blend.py`	Adds napari-compatible-ish GL blending state helper for multi-volume compositing.
`cellacdc/volume_renderer/canvas.py`	Implements the main `VolumeRendererWindow` (VisPy canvas, LUTs, labels overlay, points layers, downsampling, camera/home view).
`cellacdc/volume_renderer/_widgets.py`	Adds renderer toolbars (home/save/update + single-channel mode).
`cellacdc/volume_renderer/_demos/data/.gitkeep`	Keeps demo data folder in repo while ignoring downloaded content.
`cellacdc/volume_renderer/_demos/_demo_single_channel.py`	Demo: render a single channel from an existing dataset path.
`cellacdc/volume_renderer/_demos/_demo_single_channel_lab_3d.py`	Demo: render volume + 3D labels with voxel size.
`cellacdc/volume_renderer/_demos/_demo_single_channel_lab_3d_with_points.py`	Demo: render volume + labels + points loaded from CSV.
`cellacdc/volume_renderer/_demos/_demo_single_channel_lab_2d.py`	Demo: render 2D labels replicated along Z.
`cellacdc/volume_renderer/_demos/_demo_single_channel_custom_cmap.py`	Demo: render single channel with a custom 2-color cmap.
`cellacdc/volume_renderer/_demos/_demo_multi_channel.py`	Demo: render multi-channel overlay.
`cellacdc/volume_renderer/_demos/_demo_multi_channel_lab_3d_with_points.py`	Demo: multi-channel + labels + points.
`cellacdc/volume_renderer/_demos/_demo_lab_2d.py`	Demo: labels-only rendering.
`cellacdc/volume_renderer/__init__.py`	Exposes module-local demo `data_path`.
`cellacdc/plot.py`	Adds VisPy marker symbol typing + PyQtGraph↔VisPy symbol mapping/path lookup.
`cellacdc/myutils.py`	Adds helper to download and extract demo dataset.
`cellacdc/gui.py`	Integrates “Launch 3D viewer” action/button and syncs labels gradient shuffle signals.
`cellacdc/colors.py`	Adds typed colormap helpers and PyQtGraph→VisPy colormap conversion + auto-contrast percentile helper.
`cellacdc/apps.py`	Extends points-layer appearance dialog to support VisPy backend and optional opacity slider.
`cellacdc/__init__.py`	Attempts to import `VolumeRendererWindow` when GUI is installed (best-effort).
`.gitignore`	Ignores downloaded demo data under `cellacdc/volume_renderer/_demos/data/*` while keeping `.gitkeep`.

Comments suppressed due to low confidence (1)

cellacdc/widgets.py:3449

ToolButtonCustomColor.paintEvent always calls p.end() in finally, but p is only defined inside the try. If QPainter(self) raises, finally will raise UnboundLocalError, masking the original exception.

    def paintEvent(self, event):
        QToolButton.paintEvent(self, event)
        try:
            p = QPainter(self)
            w, h = self.width(), self.height()
            sf = 0.6
            p.scale(w*sf, h*sf)
            p.translate(0.5/sf, 0.5/sf)
            symbol = plot.PyQtGraphScatterPlotSymbolPathMatter[self.symbol]
            pen = pg.mkPen(color=self.penColor, width=2)
            brush = pg.mkBrush(color=self.brushColor)
            p.setRenderHint(QPainter.RenderHint.Antialiasing)
            p.setPen(pen)
            p.setBrush(brush)
            p.drawPath(symbol)
        except Exception as e:
            traceback.print_exc()
        finally:
            p.end()

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+        cmaps = None
+        lut_items_states = None
+        if lut_item_state is not None:
+            lut_items_states = {channel_name: cmap}
+        elif cmap is not None:
+            cmaps = {channel_name: cmap}
+
+        volumes = {channel_name: volume}
+
+        self.set_volumes(
+            volumes, 
+            cmaps=cmaps, 
+            lut_items_states=lut_items_states
+        )


+        self._voxel_size_transform = None
+        self._lab_ncolors = 256
+        self._voxel_size_strides_transform = None
+        self._downsample_strides = None
+        self._object_labels_list_buttongroup = None


ElpadoCan · 2026-07-07T16:38:24Z

+        if self._downsample_strides is None:
+            strides = tuple(
+                max(1, int(np.ceil(s / max_size))) for s in vol.shape
+            )
+            self._downsample_strides = strides
+        else:
+            strides = self._downsample_strides
+
+        if all(s == 1 for s in strides):
+            return vol
+        return np.ascontiguousarray(vol[::strides[0], ::strides[1], ::strides[2]])


While we don't guard for it, we don't allow volumes with different shapes. We will add a guard for that

+        if points_df is not None:
+            points_xyz = points_df[zyx_columns_names[::-1]].to_numpy()
+        elif points:
+            points_xyz = points[:, [2, 1, 0]]
+        else:
+            raise ValueError(
+                "Either 'points' or 'points_df' must be provided."
+            ) 


+        if not self._channels_data:
+            Z, Y, X = self._lab.shape
+            dummy_vol = np.zeros((Z, Y, X), dtype=np.float32)
+            self.set_volume(dummy_vol, channel_name='1')
+


+        for c, (channel, channel_data) in enumerate(self._channels_data.items()):
+            blending = "translucent_no_depth" if c == 0 else "additive"
+            node = channel_data.node
+            node.order = c
+            node.opacity = channel_data.opacity_slider.value()
+            node.set_gl_state(**volume_gl_state(blending, first_visible=c==0))    


+        if not checked:
+            self._volume_renderer.close()
+            self._volume_renderer = None
+            return


+    def onClose3dViewer(self):
+        self.launch3dViewerAction.setChecked(False)


ElpadoCan added 8 commits May 28, 2026 20:25

WIP: code for sub-module and main window UI

0a5483c

WIP: base UI layout, working on lut items

3bd23ba

WIP: set channels data

0fe4e67

WIP: store channels dataclass

57e6e40

WIP: correct multi-channel blending options

b9e98b3

WIP: add opacity sliders

bd63a26

WIP: add toolbutton, still missing the slot

95a4f8b

WIP: add channels toolbar button and single channel mode

4b566f6

This was referenced Jun 15, 2026

Multivolume 3d render #1110

Closed

Additional improvements 3d renderer from contributor #1106

Closed

Improvements 3d renderer #1102

Closed

ElpadoCan added 19 commits June 15, 2026 10:05

fix: import volume renderer only if GUI libraries installed

7163cc3

Merge branch 'renderer_3d_v2' of https://github.com/SchmollerLab/Cell…

492b2f9

…_ACDC into renderer_3d_v2

WIP: add labels ui items

5b167b1

WIP: adds labels volume renderer

4c322b3

WIP: overloaded set_labels

50790cc

WIP: labels node cmap on gradient change

b6513cc

WIP: selectable object labels

34134fb

feat: 3d viewer API

bc4f915

feat: add 3d viewer to gui

99dfd08

fix: set viewer camera range

3bd2acb

improvement: set and reset view as distinct methods

0ca2386

WIP: add points layer markers

78444af

WIP: adding ui items for points layer

b488152

WIP: adapting edit points layer dialog to vispy markers

c1902a3

WIP: adapting edit points layer dialog to vispy markers

3b68bff

feat: points layer with editing and removing options

e0470c0

feat: hide unselected or focus on selected diplay option

bc863c5

WIP: add points layer to volume renderer from gui

0414de6

feat: show all radio button to show raw volume

b631b2c

ElpadoCan added 8 commits July 7, 2026 11:45

chore: add multi channel demo with points

d30a553

Merge branch 'main' into renderer_3d_v2

5296ee3

fix: install PyOpenGL when running 3d viewer first time

32be2c2

WIP: fixing demo only labels

147440f

fix: check import OpenGL correctly

b012b75

fix: reset lab gradient item

4e76623

fix: lint error

75a1356

fix: view only segm labels in 3d viewer

e337e18

ElpadoCan marked this pull request as ready for review July 7, 2026 15:13

Teranis requested a review from Copilot July 7, 2026 15:31

Copilot started reviewing on behalf of Teranis July 7, 2026 15:31 View session

Copilot AI reviewed Jul 7, 2026

View reviewed changes

ElpadoCan added 2 commits July 7, 2026 17:45

Merge branch 'main' into renderer_3d_v2

47d57f3

fix: address copilot comments

40eba5a

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Volume Renderer v2#1120

Volume Renderer v2#1120
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ElpadoCan commented Jun 15, 2026 •

edited

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		def onClose3dViewer(self):
		self.launch3dViewerAction.setChecked(False)

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Pull request overview

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ElpadoCan Jul 7, 2026

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ElpadoCan commented Jun 15, 2026 •

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