Support zarr 3

pyproject.toml

@@ -33,13 +33,13 @@ classifiers = [# https://pypi.python.org/pypi?%3Aaction=list_classifiers
 dependencies = [
     "adjustText",
     "anndata>=0.12.4", # https://github.com/scverse/anndata/issues/2166
-    "bioio<2",
+    "bioio",
     "bioio-nd2",
     "bioio-tifffile",
     "centrosome",
     "cp-measure>=0.1.16",
     "dask-image",
-    "dask<=2025.11.0",
+    "dask!=2026.1.1,!=2026.1.0,!=2025.12.0", # ignores keyword arguments in da.to_zarr
     "decorator",
     "filelock",
     "flox",
@@ -54,7 +54,7 @@ dependencies = [
     "natsort",
     "numcodecs",
     "numpy",
-    "ome-zarr<0.12.0",
+    "ome-zarr",
     "pandas",
     "pint",
     "psutil",
@@ -68,9 +68,9 @@ dependencies = [
     "stardist",
     "statsmodels",
     "tensorflow",
-    "tifffile<=2025.5.10",
+    "tifffile",
     "xarray",
-    "zarr<3"
+    "zarr>=3"
 ]
 
 [project.optional-dependencies]

requirements.doc.txt

@@ -1,4 +1,4 @@
-ipython==9.9.0
+ipython==9.10.0
 nbsphinx==0.9.8
 sphinx-copybutton==0.5.2
 sphinx==9.1.0

requirements.txt

@@ -1,13 +1,15 @@
 anndata==0.12.10
 adjustText==1.3.0
-bioio-nd2==1.3.0
+bioio==3.3.0
+bioio-nd2==1.7.0
+bioio-ome-tiff==1.4.0
+bioio-ome-zarr==3.3.0
 bioio-tifffile==1.3.0
-bioio==1.6.1
 centrosome==1.3.3
 cp-measure==0.1.16
 cython==3.2.4
 dask-image==2025.11.0
-dask==2025.11.0
+dask==2025.12.0
 decorator==5.2.1
 filelock==3.25.2
 flox==0.11.2
@@ -20,9 +22,9 @@ kneed==0.8.6
 mahotas==1.4.18
 matplotlib==3.10.8
 natsort==8.4.0
-numcodecs==0.15.1
+numcodecs==0.16.5
 numpy==2.4.4
-ome-zarr==0.11.1
+ome-zarr==0.14.0
 pandas==2.3.3
 pint==0.25.3
 psutil==7.2.2
@@ -36,6 +38,6 @@ shapely==2.1.2
 stardist==0.9.2
 statsmodels==0.14.6
 tensorflow==2.21.0
-tifffile==2025.5.10
+tifffile==2026.3.3
 xarray==2026.2.0
-zarr==2.18.7
+zarr==3.1.6