Update Cellier version

.github/workflows/ci.yml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12", "3.13",]
+        python-version: ["3.12", "3.13",]
         platform: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
@@ -86,7 +86,7 @@ jobs:
       - uses: actions/checkout@v7
         with:
           fetch-depth: 0
-      - uses: hynek/build-and-inspect-python-package@v2
+      - uses: hynek/build-and-inspect-python-package@2abe76da66d0a6a4a227101f9348ee855797cfa5 # v3.0.1
 
   upload-to-pypi:
     name: Upload package to PyPI

README.md

@@ -33,6 +33,12 @@ You can load a v0.4 or v0.5 OME-Zarr file into a single-canvas 2d/3d viewer usin
 oz-viewer view path/to/image.ome.zarr
 ```
 
+Note that some OME-Zarr files do not provide the necessary translation in the multiscale transforms to keep the downscaled voxels centered. `oz-viewer` provides a flag to infer the translations based on the shapes and downscale factors of the multiscale levels. Use the `--infer-multiscale-translations` flag to enable this behavior.
+
+```sh
+oz-viewer view path/to/image.ome.zarr --infer-multiscale-translations`
+```
+
 Example viewing a https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpA_VIP_ASLM_on.zarr (1937, 2048, 2048), anisotropic voxels (file was on local SSD).
 
 https://github.com/user-attachments/assets/59c31e89-db42-4cec-ae4f-373d997c227f
@@ -45,11 +51,18 @@ You can load a v0.4 or v0.5 OME-Zarr file into an orthoviewer using the `oz-view
 oz-viewer ortho path/to/image.ome.zarr
 ```
 
+Note that some OME-Zarr files do not provide the necessary translation in the multiscale transforms to keep the downscaled voxels centered. `oz-viewer` provides a flag to infer the translations based on the shapes and downscale factors of the multiscale levels. Use the `--infer-multiscale-translations` flag to enable this behavior.
+
+```sh
+oz-viewer ortho path/to/image.ome.zarr --infer-multiscale-translations`
+```
+
+
 Example viewing https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpA_VIP_ASLM_on.zarr (1937, 2048, 2048), anisotropic voxels (file was on local SSD).
 
 https://github.com/user-attachments/assets/a6c0cab9-0cd9-4fe0-80c2-c77207b4fd77
 
-You can click the multichannel button in the upper left-hand corner to toggle between single/multichannel rendering. Example viewing the scikit-image cells3d (converted to ome-zarr) multichannel image
+Images with a channel axis open as a composite of their channels (up to 4). Use the "Composite channels" checkbox in the image controls on the left to switch between the composite and single-channel rendering, where a slider steps through the channels. Example viewing the scikit-image cells3d (converted to ome-zarr) multichannel image
 
 https://github.com/user-attachments/assets/b6655863-b8fb-4eea-be84-eb031283494e
 

pyproject.toml

@@ -19,15 +19,14 @@ name = "oz-viewer"
 dynamic = ["version"]
 description = "A viewer for ome-zarr images."
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 license = { text = "BSD-3-Clause" }
 authors = [{ name = "Kevin Yamauchi", email = "kevin.yamauchi@gmail.com" }]
 # https://pypi.org/classifiers/
 classifiers = [
     "Development Status :: 3 - Alpha",
     "License :: OSI Approved :: BSD License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Typing :: Typed",
@@ -38,7 +37,7 @@ dependencies = [
     "typer >= 0.12",
     "rich >= 13",
     "numpy >= 1.24",
-    "cellier[pyside,anywidget]>=0.0.26",
+    "cellier[pyside,anywidget]>=0.0.27",
     "aiohttp >= 3.9",
     "zarr >= 3.0",
     "s3fs",
@@ -49,15 +48,6 @@ dependencies = [
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 # add dependencies for "extra" features here.  Not dev dependencies.
 [project.optional-dependencies]
-# Dependencies for the notebook examples under examples/.  Install with
-# `pip install -e '.[examples]'`.  cellier[anywidget] adds the anywidget
-# front-end (notebook rendering); scikit-image + pooch provide the cells3d
-# sample dataset used by examples/viewer.ipynb.
-#
-# NOTE: the anywidget canvas backend currently requires rendercanvas from git
-# main, which cannot be expressed as a version pin here -- install it
-# separately:
-#   uv pip install "rendercanvas @ git+https://github.com/pygfx/rendercanvas.git"
 examples = [
     "jupyterlab>=4.5.6",
     "scikit-image>=0.24",

src/oz_viewer/_cli.py

@@ -157,6 +157,19 @@ def ortho(
             show_default=False,
         ),
     ] = None,
+    infer_multiscale_translations: Annotated[
+        bool,
+        typer.Option(
+            "--infer-multiscale-translations",
+            help=(
+                "Assume the coarser pyramid levels were downsampled centre-aligned"
+                " (e.g. block averages) and add the half-voxel offsets that implies"
+                " when the store declares no level translations. Wrong for"
+                " pyramids made by striding. Ignored, with a warning, when the"
+                " store declares translations."
+            ),
+        ),
+    ] = False,
     theme: Annotated[
         str,
         typer.Option(
@@ -237,7 +250,13 @@ def ortho(
         perf.mark("cli.ortho.uri_resolved", zarr_uri=zarr_uri)
 
     perf.mark("cli.ortho.launch")
-    launch_orthoviewer(zarr_uri, channel_axis=multichannel, theme=theme, perf=perf)
+    launch_orthoviewer(
+        zarr_uri,
+        channel_axis=multichannel,
+        infer_multiscale_translations=infer_multiscale_translations,
+        theme=theme,
+        perf=perf,
+    )
 
 
 @app.command()
@@ -279,6 +298,19 @@ def view(
             show_default=False,
         ),
     ] = None,
+    infer_multiscale_translations: Annotated[
+        bool,
+        typer.Option(
+            "--infer-multiscale-translations",
+            help=(
+                "Assume the coarser pyramid levels were downsampled centre-aligned"
+                " (e.g. block averages) and add the half-voxel offsets that implies"
+                " when the store declares no level translations. Wrong for"
+                " pyramids made by striding. Ignored, with a warning, when the"
+                " store declares translations."
+            ),
+        ),
+    ] = False,
     theme: Annotated[
         str,
         typer.Option(
@@ -359,7 +391,13 @@ def view(
         perf.mark("cli.view.uri_resolved", zarr_uri=zarr_uri)
 
     perf.mark("cli.view.launch")
-    launch_viewer(zarr_uri, channel_axis=multichannel, theme=theme, perf=perf)
+    launch_viewer(
+        zarr_uri,
+        channel_axis=multichannel,
+        infer_multiscale_translations=infer_multiscale_translations,
+        theme=theme,
+        perf=perf,
+    )
 
 
 @app.command(name="theme")