diff --git a/.github/workflows/credit.yml b/.github/workflows/credit.yml
index 9e6aa00b663..3ceb98a185d 100644
--- a/.github/workflows/credit.yml
+++ b/.github/workflows/credit.yml
@@ -40,6 +40,6 @@ jobs:
           git checkout -b credit
           git commit -am "MAINT: Update code credit"
           git push origin credit
-          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to `doc/changes/credit_tools.py` or `.mailmap` etc. to get CircleCI to pass.*" --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head credit --title "MAINT: Update code credit" --body "Created by credit [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to \`doc/changes/credit_tools.py\` or \`.mailmap\` etc. to get CircleCI to pass.*" --label "no-changelog-entry-needed")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'
diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml
index 3f3698190fc..6a45f2876b6 100644
--- a/.github/workflows/spec_zero.yml
+++ b/.github/workflows/spec_zero.yml
@@ -57,6 +57,6 @@ jobs:
           git checkout -b spec_zero
           git commit -am "MAINT: Update dependency specifiers"
           git push origin spec_zero
-          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in mne/fixes.py in this or another PR. `git grep TODO VERSION` is a good starting point for finding potential updates.*" --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in \`mne/fixes.py\` in this or another PR. \`git grep TODO VERSION\` is a good starting point for finding potential updates.*" --label "no-changelog-entry-needed")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 04b22145319..7eefe5d0941 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.2
+    rev: v0.14.3
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.16.0
+    rev: v1.16.2
     hooks:
       - id: zizmor
 
diff --git a/doc/changes/dev/13468.bugfix.rst b/doc/changes/dev/13468.bugfix.rst
new file mode 100644
index 00000000000..162ee90ff6a
--- /dev/null
+++ b/doc/changes/dev/13468.bugfix.rst
@@ -0,0 +1 @@
+Correctly set the calibration factor in Nihon Kohden reader (which affects channel amplitudes), by `Tom Ma`_.
diff --git a/doc/changes/dev/13478.bugfix.rst b/doc/changes/dev/13478.bugfix.rst
new file mode 100644
index 00000000000..426f0ba5a91
--- /dev/null
+++ b/doc/changes/dev/13478.bugfix.rst
@@ -0,0 +1 @@
+Fix bug with :func:`mne.preprocessing.ICA.apply` not working when the ICA instance was fitted including marked bad channels, by `Michael Straube`_.
\ No newline at end of file
diff --git a/doc/conf.py b/doc/conf.py
index 0c8f65b7df7..350f0d230e8 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -657,6 +657,7 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
 linkcheck_ignore = [  # will be compiled to regex
     # 403 Client Error: Forbidden
     "https://doi.org/10.1002/",  # onlinelibrary.wiley.com/doi/10.1002/hbm
+    "https://doi.org/10.1017/",  # cambridge.org
     "https://doi.org/10.1016/",  # neuroimage
     "https://doi.org/10.1021/",  # pubs.acs.org/doi/abs
     "https://doi.org/10.1063/",  # pubs.aip.org/aip/jap
@@ -682,6 +683,9 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     "https://doi.org/10.3390/",  # mdpi.com
     "https://hms.harvard.edu/",  # doc/funding.rst
     "https://stackoverflow.com/questions/21752259/python-why-pickle",  # doc/help/faq
+    "https://blender.org",
+    "https://home.alexk101.dev",
+    "https://www.mq.edu.au/",
     "https://www.biorxiv.org/content/10.1101/",  # biorxiv.org
     "https://www.researchgate.net/profile/",
     "https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html",
@@ -746,13 +750,10 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
 show_warning_types = True
 nitpick_ignore = [
     ("py:class", "None.  Remove all items from D."),
-    ("py:class", "a set-like object providing a view on D's items"),
-    ("py:class", "a set-like object providing a view on D's keys"),
     (
         "py:class",
         "v, remove specified key and return the corresponding value.",
     ),  # noqa: E501
-    ("py:class", "None.  Update D from dict/iterable E and F."),
     ("py:class", "an object providing a view on D's values"),
     ("py:class", "a shallow copy of D"),
     ("py:class", "(k, v), remove and return some (key, value) pair as a"),
@@ -761,6 +762,8 @@ def fix_sklearn_inherited_docstrings(app, what, name, obj, options, lines):
     ("py:class", "None.  Remove all items from od."),
 ]
 nitpick_ignore_regex = [
+    ("py:class", "a set-like object providing a view on D's (items|keys)"),
+    ("py:class", r"None\.  Update D from (dict|mapping)/iterable E and F\."),
     # Classes whose methods we purposefully do not document
     ("py:.*", r"mne\.io\.BaseRaw.*"),  # use mne.io.Raw
     ("py:.*", r"mne\.BaseEpochs.*"),  # use mne.Epochs
diff --git a/doc/sphinxext/prs/13096.json b/doc/sphinxext/prs/13096.json
new file mode 100644
index 00000000000..6b04f0c57cd
--- /dev/null
+++ b/doc/sphinxext/prs/13096.json
@@ -0,0 +1,51 @@
+{
+  "merge_commit_sha": "c4de9b61cd5f40a8771a853d483621c735390ec2",
+  "authors": [
+    {
+      "n": "Young Truong",
+      "e": null
+    },
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Bru",
+      "e": "b.aristimunha@gmail.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    "doc/changes/dev/13096.newfeature.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/io/eeglab/_eeglab.py": {
+      "a": 195,
+      "d": 7
+    },
+    "mne/io/eeglab/eeglab.py": {
+      "a": 63,
+      "d": 23
+    },
+    "mne/io/eeglab/tests/test_eeglab.py": {
+      "a": 143,
+      "d": 2
+    },
+    "tools/azure_dependencies.sh": {
+      "a": 3,
+      "d": 1
+    },
+    "tools/github_actions_dependencies.sh": {
+      "a": 4,
+      "d": 0
+    },
+    "tools/github_actions_env_vars.sh": {
+      "a": 1,
+      "d": 1
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13251.json b/doc/sphinxext/prs/13251.json
new file mode 100644
index 00000000000..de9b32ad434
--- /dev/null
+++ b/doc/sphinxext/prs/13251.json
@@ -0,0 +1,39 @@
+{
+  "merge_commit_sha": "181fea1e7e0bd73c2ec5cf67391cf598ad1af7bf",
+  "authors": [
+    {
+      "n": null,
+      "e": "myd7349@gmail.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    ".github/workflows/tests.yml": {
+      "a": 1,
+      "d": 0
+    },
+    "azure-pipelines.yml": {
+      "a": 1,
+      "d": 0
+    },
+    "doc/changes/dev/13251.bugfix.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/datasets/config.py": {
+      "a": 2,
+      "d": 2
+    },
+    "mne/io/nihon/nihon.py": {
+      "a": 55,
+      "d": 11
+    },
+    "mne/io/nihon/tests/test_nihon.py": {
+      "a": 8,
+      "d": 10
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13347.json b/doc/sphinxext/prs/13347.json
new file mode 100644
index 00000000000..e6dcebc212f
--- /dev/null
+++ b/doc/sphinxext/prs/13347.json
@@ -0,0 +1,19 @@
+{
+  "merge_commit_sha": "94d9871acc920a47a04e9481d1fb2dfb25be7bfe",
+  "authors": [
+    {
+      "n": "Clemens Brunner",
+      "e": null
+    },
+    {
+      "n": "Daniel McCloy",
+      "e": "dan@mccloy.info"
+    }
+  ],
+  "changes": {
+    "doc/conf.py": {
+      "a": 16,
+      "d": 4
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13421.json b/doc/sphinxext/prs/13421.json
new file mode 100644
index 00000000000..cc10cbda0be
--- /dev/null
+++ b/doc/sphinxext/prs/13421.json
@@ -0,0 +1,27 @@
+{
+  "merge_commit_sha": "52234feffb2d46ebcc7d204697ec9bec15fd6d75",
+  "authors": [
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    "tools/azure_dependencies.sh": {
+      "a": 1,
+      "d": 3
+    },
+    "tools/github_actions_dependencies.sh": {
+      "a": 0,
+      "d": 4
+    },
+    "tools/github_actions_env_vars.sh": {
+      "a": 1,
+      "d": 1
+    },
+    "tools/install_pre_requirements.sh": {
+      "a": 2,
+      "d": 0
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13431.json b/doc/sphinxext/prs/13431.json
new file mode 100644
index 00000000000..f8fb6f633f9
--- /dev/null
+++ b/doc/sphinxext/prs/13431.json
@@ -0,0 +1,59 @@
+{
+  "merge_commit_sha": "34e2743d7f1a1684f6359520392fd437bf2cd92f",
+  "authors": [
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    ".github/workflows/tests.yml": {
+      "a": 13,
+      "d": 7
+    },
+    ".pre-commit-config.yaml": {
+      "a": 2,
+      "d": 2
+    },
+    "doc/sphinxext/related_software.py": {
+      "a": 0,
+      "d": 1
+    },
+    "environment.yml": {
+      "a": 2,
+      "d": 0
+    },
+    "mne/conftest.py": {
+      "a": 5,
+      "d": 0
+    },
+    "mne/decoding/tests/test_receptive_field.py": {
+      "a": 2,
+      "d": 2
+    },
+    "mne/viz/backends/_pyvista.py": {
+      "a": 3,
+      "d": 0
+    },
+    "mne/viz/backends/tests/test_renderer.py": {
+      "a": 1,
+      "d": 0
+    },
+    "tools/circleci_dependencies.sh": {
+      "a": 1,
+      "d": 1
+    },
+    "tools/github_actions_dependencies.sh": {
+      "a": 2,
+      "d": 0
+    },
+    "tools/hooks/update_environment_file.py": {
+      "a": 2,
+      "d": 5
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13432.json b/doc/sphinxext/prs/13432.json
new file mode 100644
index 00000000000..a1f9475b5c1
--- /dev/null
+++ b/doc/sphinxext/prs/13432.json
@@ -0,0 +1,91 @@
+{
+  "merge_commit_sha": "51b6a5c5fe711d10e959f1669960b4506cb4ad6e",
+  "authors": [
+    {
+      "n": "github-actions[bot]",
+      "e": "41898282+github-actions[bot]@users.noreply.github.com"
+    }
+  ],
+  "changes": {
+    "doc/sphinxext/prs/13350.json": {
+      "a": 51,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13375.json": {
+      "a": 27,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13395.json": {
+      "a": 27,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13398.json": {
+      "a": 75,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13403.json": {
+      "a": 107,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13404.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13405.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13407.json": {
+      "a": 107,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13409.json": {
+      "a": 47,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13410.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13411.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13412.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13413.json": {
+      "a": 19,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13416.json": {
+      "a": 27,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13420.json": {
+      "a": 19,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13423.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13424.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13426.json": {
+      "a": 31,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13427.json": {
+      "a": 15,
+      "d": 0
+    },
+    "doc/sphinxext/prs/13428.json": {
+      "a": 35,
+      "d": 0
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13434.json b/doc/sphinxext/prs/13434.json
new file mode 100644
index 00000000000..3995a187bc2
--- /dev/null
+++ b/doc/sphinxext/prs/13434.json
@@ -0,0 +1,31 @@
+{
+  "merge_commit_sha": "4fdde3a1cc87c66263d9b0c663d6a81abfcd89b5",
+  "authors": [
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    ".pre-commit-config.yaml": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/conftest.py": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/preprocessing/tests/test_maxwell.py": {
+      "a": 7,
+      "d": 0
+    },
+    "tools/install_pre_requirements.sh": {
+      "a": 7,
+      "d": 1
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13435.json b/doc/sphinxext/prs/13435.json
new file mode 100644
index 00000000000..fba54c8e7a7
--- /dev/null
+++ b/doc/sphinxext/prs/13435.json
@@ -0,0 +1,47 @@
+{
+  "merge_commit_sha": "61bc8b8755da982491d4cebf940bbde160b98e1a",
+  "authors": [
+    {
+      "n": "Clemens Brunner",
+      "e": null
+    },
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    "doc/changes/dev/13435.newfeature.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "environment.yml": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/conftest.py": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/export/_edf_bdf.py": {
+      "a": 75,
+      "d": 34
+    },
+    "mne/export/_export.py": {
+      "a": 22,
+      "d": 16
+    },
+    "mne/export/tests/test_export.py": {
+      "a": 48,
+      "d": 0
+    },
+    "pyproject.toml": {
+      "a": 2,
+      "d": 2
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13436.json b/doc/sphinxext/prs/13436.json
new file mode 100644
index 00000000000..e42a8e1f9e8
--- /dev/null
+++ b/doc/sphinxext/prs/13436.json
@@ -0,0 +1,27 @@
+{
+  "merge_commit_sha": "f7df4e5cc88bfb6795932ebbd7a3e72fdaff39d1",
+  "authors": [
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    ".github/workflows/check_changelog.yml": {
+      "a": 4,
+      "d": 1
+    },
+    "mne/datasets/tests/test_datasets.py": {
+      "a": 3,
+      "d": 3
+    },
+    "mne/surface.py": {
+      "a": 3,
+      "d": 8
+    },
+    "tools/install_pre_requirements.sh": {
+      "a": 1,
+      "d": 7
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13437.json b/doc/sphinxext/prs/13437.json
new file mode 100644
index 00000000000..d522701eb73
--- /dev/null
+++ b/doc/sphinxext/prs/13437.json
@@ -0,0 +1,43 @@
+{
+  "merge_commit_sha": "49b09fb6e0f6353f49239ee7a35a08b955c496ac",
+  "authors": [
+    {
+      "n": "Clemens Brunner",
+      "e": null
+    },
+    {
+      "n": "pre-commit-ci[bot]",
+      "e": "66853113+pre-commit-ci[bot]@users.noreply.github.com"
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    "environment.yml": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/conftest.py": {
+      "a": 1,
+      "d": 1
+    },
+    "mne/export/_edf_bdf.py": {
+      "a": 75,
+      "d": 34
+    },
+    "mne/export/_export.py": {
+      "a": 22,
+      "d": 16
+    },
+    "mne/export/tests/test_export.py": {
+      "a": 48,
+      "d": 0
+    },
+    "pyproject.toml": {
+      "a": 2,
+      "d": 2
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13439.json b/doc/sphinxext/prs/13439.json
new file mode 100644
index 00000000000..c1b249d43df
--- /dev/null
+++ b/doc/sphinxext/prs/13439.json
@@ -0,0 +1,15 @@
+{
+  "merge_commit_sha": "adc01cdc40cdaaf00d39108923dce352bd3091b2",
+  "authors": [
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    ".circleci/config.yml": {
+      "a": 2,
+      "d": 1
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13440.json b/doc/sphinxext/prs/13440.json
new file mode 100644
index 00000000000..480fdfa9bbb
--- /dev/null
+++ b/doc/sphinxext/prs/13440.json
@@ -0,0 +1,63 @@
+{
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new file mode 100644
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index 00000000000..b2634e21f57
--- /dev/null
+++ b/doc/sphinxext/prs/13470.json
@@ -0,0 +1,23 @@
+{
+  "merge_commit_sha": "f09b3da1a23757b76fd0adfdb9c6ed29db14af29",
+  "authors": [
+    {
+      "n": "Michael Straube",
+      "e": null
+    },
+    {
+      "n": "Eric Larson",
+      "e": "larson.eric.d@gmail.com"
+    }
+  ],
+  "changes": {
+    "doc/changes/dev/13470.bugfix.rst": {
+      "a": 1,
+      "d": 0
+    },
+    "mne/viz/topomap.py": {
+      "a": 2,
+      "d": 5
+    }
+  }
+}
\ No newline at end of file
diff --git a/doc/sphinxext/prs/13475.json b/doc/sphinxext/prs/13475.json
new file mode 100644
index 00000000000..fc952399543
--- /dev/null
+++ b/doc/sphinxext/prs/13475.json
@@ -0,0 +1,15 @@
+{
+  "merge_commit_sha": "1815534a3252faf159594ae5d9480b529ab9fb3d",
+  "authors": [
+    {
+      "n": "Daniel McCloy",
+      "e": null
+    }
+  ],
+  "changes": {
+    ".mailmap": {
+      "a": 1,
+      "d": 1
+    }
+  }
+}
\ No newline at end of file
diff --git a/mne/datasets/config.py b/mne/datasets/config.py
index 53bea629097..62937779692 100644
--- a/mne/datasets/config.py
+++ b/mne/datasets/config.py
@@ -87,7 +87,7 @@
 # update the checksum in the MNE_DATASETS dict below, and change version
 # here: ↓↓↓↓↓↓↓↓
 RELEASES = dict(
-    testing="0.166",
+    testing="0.167",
     misc="0.27",
     phantom_kit="0.2",
     ucl_opm_auditory="0.2",
@@ -115,7 +115,7 @@
 # Testing and misc are at the top as they're updated most often
 MNE_DATASETS["testing"] = dict(
     archive_name=f"{TESTING_VERSIONED}.tar.gz",
-    hash="md5:273c5919cf74198a39146e9cbc146ce0",
+    hash="md5:d82318a83b436ca2c7ca8420487c05c2",
     url=(
         "https://codeload.github.com/mne-tools/mne-testing-data/"
         f"tar.gz/{RELEASES['testing']}"
diff --git a/mne/io/nihon/nihon.py b/mne/io/nihon/nihon.py
index 91db6a083d2..0c474a4b250 100644
--- a/mne/io/nihon/nihon.py
+++ b/mne/io/nihon/nihon.py
@@ -162,9 +162,14 @@ def _read_21e_file(fname):
                 break
         else:
             warn(
-                f"Could not decode 21E file as one of {_encodings}; "
+                f"Could not decode {e_fname} as one of {_encodings}; "
                 f"Default channel names are chosen."
             )
+    else:
+        warn(
+            f"Could not find {e_fname} containing channel definitions; "
+            f"Default channel names are chosen."
+        )
 
     return _chan_labels
 
@@ -280,7 +285,7 @@ def _read_nihon_header(fname):
                     "Cannot read NK file with different sfreq in each datablock"
                 )
 
-    return header
+    return header, _chan_labels
 
 
 def _read_event_log_block(fid, t_block, version):
@@ -380,13 +385,13 @@ def _map_ch_to_type(ch_name):
     return "eeg"
 
 
-def _map_ch_to_specs(ch_name):
+def _map_ch_to_specs(ch_name, chan_labels_upper):
     unit_mult = 1e-3
     phys_min = -12002.9
     phys_max = 12002.56
     dig_min = -32768
-    if ch_name.upper() in _default_chan_labels:
-        idx = _default_chan_labels.index(ch_name.upper())
+    if ch_name.upper() in chan_labels_upper:
+        idx = chan_labels_upper.index(ch_name.upper())
         if (idx < 42 or idx > 73) and idx not in [76, 77]:
             unit_mult = 1e-6
             phys_min = -3200
@@ -432,7 +437,9 @@ def __init__(self, fname, preload=False, *, encoding="utf-8", verbose=None):
         data_name = fname.name
         logger.info(f"Loading {data_name}")
 
-        header = _read_nihon_header(fname)
+        # chan_labels are electrode codes defined in the .21E file.
+        # It is not the same as header["ch_names"].
+        header, chan_labels = _read_nihon_header(fname)
         metadata = _read_nihon_metadata(fname)
 
         # n_chan = len(header['ch_names']) + 1
@@ -447,8 +454,9 @@ def __init__(self, fname, preload=False, *, encoding="utf-8", verbose=None):
         if "meas_date" in metadata:
             with info._unlock():
                 info["meas_date"] = metadata["meas_date"]
-        chs = {x: _map_ch_to_specs(x) for x in info["ch_names"]}
 
+        chan_labels_upper = [x.upper() for x in chan_labels]
+        chs = {x: _map_ch_to_specs(x, chan_labels_upper) for x in info["ch_names"]}
         cal = np.array([chs[x]["cal"] for x in info["ch_names"]], float)[:, np.newaxis]
         offsets = np.array([chs[x]["offset"] for x in info["ch_names"]], float)[
             :, np.newaxis
diff --git a/mne/io/nihon/tests/test_nihon.py b/mne/io/nihon/tests/test_nihon.py
index ba3bc204d2c..28996cfb49a 100644
--- a/mne/io/nihon/tests/test_nihon.py
+++ b/mne/io/nihon/tests/test_nihon.py
@@ -30,7 +30,7 @@ def test_nihon_eeg():
     raw_edf.drop_channels(["Events/Markers"])
 
     assert raw._data.shape == raw_edf._data.shape
-    assert raw.info["sfreq"] == raw.info["sfreq"]
+    assert raw.info["sfreq"] == raw_edf.info["sfreq"]
     # a couple of ch names differ in the EDF
     edf_ch_names = {"EEG Mark1": "$A2", "EEG Mark2": "$A1"}
     raw_edf.rename_channels(edf_ch_names)
@@ -48,7 +48,7 @@ def test_nihon_eeg():
         raw = read_raw_nihon(fname_edf, preload=True)
 
     with pytest.raises(ValueError, match="Not a valid Nihon Kohden EEG file"):
-        raw = _read_nihon_header(fname_edf)
+        header, _ = _read_nihon_header(fname_edf)
 
     bad_fname = data_path / "eximia" / "text_eximia.nxe"
 
@@ -90,3 +90,38 @@ def return_channel_duplicates(fname):
     )
     with pytest.warns(RuntimeWarning, match=msg):
         read_raw_nihon(fname)
+
+
+@testing.requires_testing_data
+def test_nihon_calibration():
+    """Test handling of calibration factor and range in Nihon Kohden EEG files."""
+    fname = data_path / "NihonKohden" / "DA00100E.EEG"
+    raw = read_raw_nihon(fname, preload=True, encoding="cp936")
+
+    Fp1_idx = raw.ch_names.index("Fp1")
+    M1_idx = raw.ch_names.index("M1")
+    M2_idx = raw.ch_names.index("M2")
+
+    Fp1_info = raw.info["chs"][Fp1_idx]
+    M1_info = raw.info["chs"][M1_idx]
+    M2_info = raw.info["chs"][M2_idx]
+
+    # M1, M2 are EEG channels, just like Fp1.
+    # So they should have the same calibration factor and physical range.
+    assert_allclose(M1_info["cal"], Fp1_info["cal"])
+    assert_allclose(M2_info["cal"], Fp1_info["cal"])
+    assert_allclose(M1_info["range"], Fp1_info["range"])
+    assert_allclose(M2_info["range"], Fp1_info["range"])
+
+    fname_edf = data_path / "NihonKohden" / "DA00100E.EDF"
+    raw_edf = read_raw_edf(fname_edf, preload=True)
+    raw_edf.drop_channels(["Events/Markers"])
+    # a couple of ch names differ in the EDF
+    edf_ch_names = {"EEG Mark1": "$M1", "EEG Mark2": "$M2"}
+    raw_edf.rename_channels(edf_ch_names)
+
+    assert raw.ch_names == raw_edf.ch_names
+    assert raw._data.shape == raw_edf._data.shape
+    assert raw.info["sfreq"] == raw_edf.info["sfreq"]
+
+    assert_allclose(raw.get_data(), raw_edf.get_data())
diff --git a/mne/preprocessing/ica.py b/mne/preprocessing/ica.py
index 1ebe20a32fe..6805007927e 100644
--- a/mne/preprocessing/ica.py
+++ b/mne/preprocessing/ica.py
@@ -2286,7 +2286,7 @@ def _apply_raw(self, raw, include, exclude, n_pca_components, start, stop):
         start, stop = _check_start_stop(raw, start, stop)
 
         picks = pick_types(
-            raw.info, meg=False, include=self.ch_names, exclude="bads", ref_meg=False
+            raw.info, meg=False, include=self.ch_names, exclude=[], ref_meg=False
         )
 
         data = raw[picks, start:stop][0]
@@ -2300,7 +2300,7 @@ def _apply_epochs(self, epochs, include, exclude, n_pca_components):
         _check_preload(epochs, "ica.apply")
 
         picks = pick_types(
-            epochs.info, meg=False, ref_meg=False, include=self.ch_names, exclude="bads"
+            epochs.info, meg=False, ref_meg=False, include=self.ch_names, exclude=[]
         )
 
         # special case where epochs come picked but fit was 'unpicked'.
@@ -2323,7 +2323,7 @@ def _apply_epochs(self, epochs, include, exclude, n_pca_components):
     def _apply_evoked(self, evoked, include, exclude, n_pca_components):
         """Aux method."""
         picks = pick_types(
-            evoked.info, meg=False, ref_meg=False, include=self.ch_names, exclude="bads"
+            evoked.info, meg=False, ref_meg=False, include=self.ch_names, exclude=[]
         )
 
         # special case where evoked come picked but fit was 'unpicked'.
diff --git a/mne/preprocessing/tests/test_ica.py b/mne/preprocessing/tests/test_ica.py
index 91dffe93078..ab8d401e019 100644
--- a/mne/preprocessing/tests/test_ica.py
+++ b/mne/preprocessing/tests/test_ica.py
@@ -1024,6 +1024,15 @@ def f(x, y):
     ica = ICA(n_components=0.99, max_iter="auto")
     ica.fit(raw_, picks=picks, reject_by_annotation=True)
 
+    # test apply when fit was run including marked bad channels
+    epochs_ = Epochs(
+        raw=raw_, events=make_fixed_length_events(raw_), baseline=None, preload=True
+    )
+    evoked_ = epochs_.average()
+    ica.apply(raw_)
+    ica.apply(epochs_)
+    ica.apply(evoked_)
+
 
 def test_get_explained_variance_ratio(tmp_path, short_raw_epochs):
     """Test ICA.get_explained_variance_ratio()."""
diff --git a/pyproject.toml b/pyproject.toml
index d612eb553bc..38ec45e76f0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,8 +20,10 @@ doc = [
   "pydata_sphinx_theme >= 0.15.2",
   "pygments >= 2.13",
   "pytest",
+  "pyvistaqt",
   "pyxdf",
   "pyzmq != 24.0.0",
+  "scikit-learn",
   "seaborn != 0.11.2",
   "selenium >= 4.27.1",
   "sphinx >= 6",
diff --git a/tutorials/io/60_ctf_bst_auditory.py b/tutorials/io/60_ctf_bst_auditory.py
index a9d86594669..4c3249996aa 100644
--- a/tutorials/io/60_ctf_bst_auditory.py
+++ b/tutorials/io/60_ctf_bst_auditory.py
@@ -16,10 +16,6 @@
     - Each run contains 200 regular beeps and 40 easy deviant beeps.
     - Random ISI: between 0.7s and 1.7s seconds, uniformly distributed.
     - Button pressed when detecting a deviant with the right index finger.
-
-The specifications of this dataset were discussed initially on the
-`FieldTrip bug tracker
-<http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2300>`__.
 """
 # Authors: Mainak Jas <mainak.jas@telecom-paristech.fr>
 #          Eric Larson <larson.eric.d@gmail.com>