diff --git a/CHANGES.rst b/CHANGES.rst
index da8985927e..5d1a789309 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,3 +1,14 @@
+2.14.0 (September 22, 2025)
+===========================
+Feature release in the 2.13.x series.
+
+This release requires a recent nitransforms release that in turn requires NumPy 2.
+Since this is a major dependency increment, a new feature release is justified.
+
+* fix: Adapt to transposed ndindex in nitransforms (#501)
+* fix: Adopt some more opinionated ruff rules, manual resolutions (#493)
+
+
 2.13.2 (July 28, 2025)
 ======================
 Patch release in the 2.13.x series.
diff --git a/env.yml b/env.yml
index c59a736884..4112d6089d 100644
--- a/env.yml
+++ b/env.yml
@@ -9,13 +9,14 @@ dependencies:
   - mkl=2024.2.2
   - mkl-service=2.4.2
   # Base scientific python stack; required by FSL, so pinned here
-  - numpy=1.26
-  - scipy=1.15
-  - matplotlib=3.9
-  - pandas=2.2
-  - h5py=3.13
+  - numpy=2.3
+  - scipy=1.16
+  - matplotlib=3.10
+  - pandas=2.3
+  - h5py=3.14
   # Dependencies compiled against numpy, best to stick with conda
   - scikit-image=0.25
+  - scikit-learn=1.7
   # Utilities
   - graphviz=11.0
   # Workflow dependencies: ANTs
diff --git a/pyproject.toml b/pyproject.toml
index 5f655cf05a..37ab4b2241 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ classifiers = [
 license = "Apache-2.0"
 requires-python = ">=3.10"
 dependencies = [
-    "acres >= 0.2.0",
+    "acres >= 0.5.0",
     "attrs >= 20.1.0",
     "nibabel >= 5.1.1",
     "nipype >= 1.9.0",
diff --git a/requirements.txt b/requirements.txt
index cc908895d2..d0dbb364b6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,35 +1,34 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --strip-extras pyproject.toml -o requirements.txt -p 3.12 -c-
-acres==0.3.0
+#    uv pip compile --strip-extras pyproject.toml -o requirements.txt -p 3.12
+acres==0.5.0
     # via
     #   sdcflows (pyproject.toml)
+    #   bidsschematools
     #   nipype
     #   nireports
     #   niworkflows
 attrs==25.3.0
     # via
     #   sdcflows (pyproject.toml)
-    #   jsonschema
     #   niworkflows
-    #   referencing
 bids-validator==1.14.7.post0
     # via pybids
-bidsschematools==1.0.4
+bidsschematools==1.1.0
     # via bids-validator
-certifi==2025.1.31
+certifi==2025.8.3
     # via requests
-charset-normalizer==3.4.1
+charset-normalizer==3.4.3
     # via requests
 ci-info==0.3.0
     # via
     #   etelemetry
     #   migas
-click==8.1.8
+click==8.3.0
     # via
     #   bidsschematools
     #   nipype
     #   pybids
-contourpy==1.3.1
+contourpy==1.3.3
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
@@ -37,19 +36,19 @@ docopt==0.6.2
     # via num2words
 etelemetry==0.3.1
     # via nipype
-filelock==3.18.0
+filelock==3.19.1
     # via nipype
-fonttools==4.56.0
+fonttools==4.60.0
     # via matplotlib
-formulaic==1.1.1
+formulaic==1.2.1
     # via pybids
 frozendict==2.4.6
     # via pybids
-fsspec==2025.3.0
+fsspec==2025.9.0
     # via universal-pathlib
-greenlet==3.1.1
+greenlet==3.2.4
     # via sqlalchemy
-h5py==3.13.0
+h5py==3.14.0
     # via nitransforms
 idna==3.10
     # via requests
@@ -57,19 +56,13 @@ imageio==2.37.0
     # via scikit-image
 interface-meta==1.3.0
     # via formulaic
-isodate==0.6.1
-    # via rdflib
 jinja2==3.1.6
     # via niworkflows
-joblib==1.4.2
+joblib==1.5.2
     # via
     #   nilearn
     #   scikit-learn
-jsonschema==4.23.0
-    # via bidsschematools
-jsonschema-specifications==2024.10.1
-    # via jsonschema
-kiwisolver==1.4.8
+kiwisolver==1.4.9
     # via matplotlib
 lazy-loader==0.4
     # via scikit-image
@@ -77,22 +70,23 @@ looseversion==1.3.0
     # via
     #   nipype
     #   niworkflows
-lxml==5.3.1
+lxml==6.0.2
     # via
     #   nilearn
     #   nireports
-    #   prov
     #   svgutils
 markupsafe==3.0.2
     # via jinja2
-matplotlib==3.9.4
+matplotlib==3.10.6
     # via
     #   nireports
     #   niworkflows
     #   seaborn
 migas==0.4.0
     # via sdcflows (pyproject.toml)
-networkx==3.4.2
+narwhals==2.5.0
+    # via formulaic
+networkx==3.5
     # via
     #   nipype
     #   prov
@@ -106,7 +100,7 @@ nibabel==5.3.2
     #   nitransforms
     #   niworkflows
     #   pybids
-nilearn==0.11.1
+nilearn==0.12.1
     # via
     #   nireports
     #   niworkflows
@@ -115,17 +109,17 @@ nipype==1.10.0
     #   sdcflows (pyproject.toml)
     #   nireports
     #   niworkflows
-nireports==25.0.1
+nireports==25.3.0
     # via sdcflows (pyproject.toml)
-nitransforms==24.1.1
+nitransforms==25.0.1
     # via
     #   sdcflows (pyproject.toml)
     #   niworkflows
-niworkflows==1.13.0
+niworkflows==1.14.1
     # via sdcflows (pyproject.toml)
 num2words==0.5.14
     # via pybids
-numpy==1.26.4
+numpy==2.3.3
     # via
     #   sdcflows (pyproject.toml)
     #   contourpy
@@ -147,7 +141,7 @@ numpy==1.26.4
     #   seaborn
     #   tifffile
     #   transforms3d
-packaging==24.2
+packaging==25.0
     # via
     #   etelemetry
     #   lazy-loader
@@ -157,7 +151,7 @@ packaging==24.2
     #   nipype
     #   niworkflows
     #   scikit-image
-pandas==2.2.3
+pandas==2.3.2
     # via
     #   formulaic
     #   nilearn
@@ -165,14 +159,14 @@ pandas==2.2.3
     #   niworkflows
     #   pybids
     #   seaborn
-pillow==11.1.0
+pillow==11.3.0
     # via
     #   imageio
     #   matplotlib
     #   scikit-image
-prov==2.0.1
+prov==2.1.1
     # via nipype
-puremagic==1.28
+puremagic==1.30
     # via nipype
 pybids==0.19.0
     # via
@@ -180,9 +174,11 @@ pybids==0.19.0
     #   nireports
     #   niworkflows
     #   templateflow
-pydot==3.0.4
-    # via nipype
-pyparsing==3.2.1
+pydot==4.0.1
+    # via
+    #   nipype
+    #   prov
+pyparsing==3.2.5
     # via
     #   matplotlib
     #   pydot
@@ -193,37 +189,27 @@ python-dateutil==2.9.0.post0
     #   nipype
     #   pandas
     #   prov
-pytz==2025.1
+pytz==2025.2
     # via pandas
 pyyaml==6.0.2
     # via
     #   bidsschematools
     #   nireports
     #   niworkflows
-rdflib==6.3.2
-    # via
-    #   nipype
-    #   prov
-referencing==0.36.2
-    # via
-    #   jsonschema
-    #   jsonschema-specifications
-requests==2.32.4
+rdflib==7.2.1
+    # via nipype
+requests==2.32.5
     # via
     #   etelemetry
     #   nilearn
     #   templateflow
-rpds-py==0.23.1
-    # via
-    #   jsonschema
-    #   referencing
 scikit-image==0.25.2
     # via
     #   sdcflows (pyproject.toml)
     #   niworkflows
-scikit-learn==1.6.1
+scikit-learn==1.7.2
     # via nilearn
-scipy==1.15.2
+scipy==1.16.2
     # via
     #   sdcflows (pyproject.toml)
     #   formulaic
@@ -241,21 +227,19 @@ seaborn==0.13.2
 simplejson==3.20.1
     # via nipype
 six==1.17.0
-    # via
-    #   isodate
-    #   python-dateutil
-sqlalchemy==2.0.39
+    # via python-dateutil
+sqlalchemy==2.0.43
     # via pybids
 svgutils==0.3.4
     # via niworkflows
-templateflow==24.2.2
+templateflow==25.0.3
     # via
     #   sdcflows (pyproject.toml)
     #   nireports
     #   niworkflows
 threadpoolctl==3.6.0
     # via scikit-learn
-tifffile==2025.3.13
+tifffile==2025.9.20
     # via scikit-image
 toml==0.10.2
     # via sdcflows (pyproject.toml)
@@ -265,17 +249,16 @@ traits==7.0.2
     # via nipype
 transforms3d==0.4.2
     # via niworkflows
-typing-extensions==4.12.2
+typing-extensions==4.15.0
     # via
     #   formulaic
     #   nibabel
-    #   referencing
     #   sqlalchemy
-tzdata==2025.1
+tzdata==2025.2
     # via pandas
 universal-pathlib==0.2.6
     # via pybids
 urllib3==2.5.0
     # via requests
-wrapt==1.17.2
+wrapt==1.17.3
     # via formulaic