diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
new file mode 100644
index 0000000..970890f
--- /dev/null
+++ b/.github/dependabot.yaml
@@ -0,0 +1,18 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: /
+  schedule:
+    interval: monthly
+  groups:
+    production-dependencies:
+      dependency-type: production
+    development-dependencies:
+      dependency-type: development
+- package-ecosystem: github-actions
+  directory: /
+  schedule:
+    interval: monthly
\ No newline at end of file
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index d7f5a95..773ee8a 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -2,13 +2,12 @@ name: CI
 
 permissions:
   contents: read
-  pull-requests: write
 
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main"]
   pull_request:
-    branches: [ "main" ]
+    branches: ["main"]
 
 env:
   UV_FROZEN: true
@@ -33,7 +32,7 @@ jobs:
     needs: format
     strategy:
       matrix:
-        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
     steps:
       - uses: actions/checkout@v6
         with:
@@ -41,6 +40,7 @@ jobs:
       - uses: astral-sh/setup-uv@v8.1.0
         with:
           python-version: ${{ matrix.python-version }}
+      - run: uv sync --all-extras
 
       - name: Run tests without cloudpathlib
         run: |
@@ -53,7 +53,7 @@ jobs:
 
       - name: Run tests with cloudpathlib
         run: |
-          uv run --extra cloud pytest \
+          uv run pytest \
             -m "cloud" \
             --junitxml=pytest-cloud.xml \
             --cov-report=xml:coverage.xml \
@@ -68,10 +68,16 @@ jobs:
             pytest-cloud.xml \
             pytest.xml
 
-      - name: Pytest coverage comment
-        if: github.event_name == 'pull_request' && matrix.python-version ==
-          env.COVERAGE_PYTHON
-        uses: MishaKav/pytest-coverage-comment@v1
+      - name: Record PR number
+        if: github.event_name == 'pull_request' && matrix.python-version == env.COVERAGE_PYTHON
+        run: echo "${{ github.event.number }}" > pr-number.txt
+
+      - uses: actions/upload-artifact@v7
+        if: github.event_name == 'pull_request' && matrix.python-version == env.COVERAGE_PYTHON
         with:
-          pytest-xml-coverage-path: ./coverage.xml
-          junitxml-path: ./pytest.xml
+          name: coverage
+          retention-days: 1
+          path: |
+            coverage.xml
+            pytest.xml
+            pr-number.txt
diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml
new file mode 100644
index 0000000..5083e10
--- /dev/null
+++ b/.github/workflows/coverage.yaml
@@ -0,0 +1,33 @@
+name: Coverage report
+
+on:
+  workflow_run:
+    workflows: ["CI"]
+    types: [completed]
+
+permissions:
+  pull-requests: write
+  actions: read
+
+jobs:
+  coverage:
+    if: >-
+      github.event.workflow_run.event == 'pull_request' &&
+      github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: coverage
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - id: pr
+        run: echo "number=$(cat pr-number.txt)" >> "$GITHUB_OUTPUT"
+
+      - name: Pytest coverage comment
+        uses: MishaKav/pytest-coverage-comment@v1
+        with:
+          issue-number: ${{ steps.pr.outputs.number }}
+          pytest-xml-coverage-path: ./coverage.xml
+          junitxml-path: ./pytest.xml
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index 07b0a3a..0eb1e63 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -1,12 +1,12 @@
-name: docs 
+name: docs
 
 on:
   workflow_run:
     workflows: [CI]
     types:
-    - completed
+      - completed
     branches:
-    - main
+      - main
 
 env:
   UV_FROZEN: true
@@ -17,16 +17,14 @@ jobs:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          pyproject-file: pyproject.toml
+        uses: astral-sh/setup-uv@v8.1.0
       - name: Install the project
         run: uv sync --all-extras
       - name: Build docs
         run: uv run pdoc -o docs/ -d google bids2table
-      - uses: actions/upload-pages-artifact@v3
+      - uses: actions/upload-pages-artifact@v5
         with:
           path: docs/
 
@@ -43,4 +41,4 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     steps:
       - id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v5
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index a05cd30..23863db 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -18,11 +18,9 @@ jobs:
       # IMPORTANT: this permission is mandatory for Trusted Publishing
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
-        with:
-          pyproject-file: pyproject.toml
+        uses: astral-sh/setup-uv@v8.1.0
       - name: Build project
         run: |
           uv sync --no-dev --no-install-project
diff --git a/bids2table/__init__.py b/bids2table/__init__.py
index 638f8db..9d94635 100644
--- a/bids2table/__init__.py
+++ b/bids2table/__init__.py
@@ -9,13 +9,16 @@
     "parse_bids_entities",
     "validate_bids_entities",
     "set_bids_schema",
+    "clear_schema_caches",
     "get_bids_schema",
     "get_bids_entity_arrow_schema",
     "format_bids_path",
     "load_bids_metadata",
     "cloudpathlib_is_available",
+    "pybids",
 ]
 
+from . import pybids
 from ._entities import (
     format_bids_path,
     get_bids_entity_arrow_schema,
@@ -26,6 +29,7 @@
 )
 from ._indexing import (
     batch_index_dataset,
+    clear_schema_caches,
     find_bids_datasets,
     get_arrow_schema,
     get_column_names,
diff --git a/bids2table/__main__.py b/bids2table/__main__.py
index bfa60c8..928dbc8 100644
--- a/bids2table/__main__.py
+++ b/bids2table/__main__.py
@@ -31,7 +31,17 @@ def main():
         nargs="+",
         default=None,
         help="List of subject names or glob patterns to only include in the index.  "
-        "Only applies when indexing a single dataset.",
+        "Deprecated; use --filter instead.",
+    )
+    parser_index.add_argument(
+        "--filter",
+        "-f",
+        metavar="ENTITY=PATTERN",
+        type=str,
+        action="append",
+        default=None,
+        help="Filter indexed files by entity value (e.g. -f sub=sub-0* -f task=rest). "
+        "Can be specified multiple times.",
     )
     parser_index.add_argument(
         "--workers",
@@ -114,10 +124,29 @@ def _index_command(args: argparse.Namespace):
         else:
             root.append(path)
 
+    # Build filters dict from --filter args
+    filters: dict[str, str | list[str]] | None = None
+    if args.filter:
+        filters = {}
+        for item in args.filter:
+            parts = item.split("=", maxsplit=1)
+            if len(parts) == 2:
+                filters[parts[0]] = parts[1]
+            else:
+                _logger.warning(
+                    f"Ignoring malformed filter: '{item}' (expected ENTITY=PATTERN)"
+                )
+
+    # Merge deprecated --subjects into filters
+    if args.subjects:
+        if filters is None:
+            filters = {}
+        filters.setdefault("sub", args.subjects)
+
     if len(root) == 1:
         table = b2t2.index_dataset(
             root[0],
-            include_subjects=args.subjects,
+            filters=filters,
             show_progress=not args.no_progress,
         )
         pq.write_table(table, args.output)
@@ -135,6 +164,7 @@ def _index_command(args: argparse.Namespace):
                 max_workers=max_workers,
                 executor_cls=executor_cls,
                 show_progress=not args.no_progress,
+                filters=filters,
             ):
                 writer.write_table(table)
 
diff --git a/bids2table/_entities.py b/bids2table/_entities.py
index ea76550..4e0f136 100644
--- a/bids2table/_entities.py
+++ b/bids2table/_entities.py
@@ -65,11 +65,9 @@
     "special": str,
 }
 
-# Matches sub-directory after subject ('sub-abc') and (optionally) session ('ses-01')
-# directories. Must be all lowercase.
-_BIDS_DATATYPE_PATTERN = re.compile(
-    r"sub-[a-zA-Z0-9]+(?:[/\\]ses-[a-zA-Z0-9]+)?[/\\]([a-z]+)[/\\]"
-)
+# Matches sub-directory after subject and (optionally) session directories.
+# Must be all lowercase. Rebuilt in set_bids_schema() once schema is loaded.
+_BIDS_DATATYPE_PATTERN: re.Pattern | None = None
 
 _logger = setup_logger(__package__)
 
@@ -77,12 +75,12 @@
 def set_bids_schema(path: str | Path | None = None) -> None:
     """Set the BIDS schema."""
     global _BIDS_SCHEMA, _BIDS_ENTITY_SCHEMA, _BIDS_NAME_ENTITY_MAP
-    global _BIDS_ENTITY_ARROW_SCHEMA
+    global _BIDS_ENTITY_ARROW_SCHEMA, _BIDS_DATATYPE_PATTERN
 
     schema = bidsschematools.schema.load_schema(path)
     entity_schema = {
         entity: schema.objects.entities[entity].to_dict()
-        for entity in schema.rules.entities
+        for entity in schema.objects.entities
     }
     # Also include special extra entities (datatype, suffix, extension).
     entity_schema.update(_BIDS_SPECIAL_ENTITY_SCHEMA)
@@ -98,6 +96,13 @@ def set_bids_schema(path: str | Path | None = None) -> None:
         schema_version=schema["schema_version"],
     )
 
+    # Build datatype pattern from entity names (e.g. sub, ses).
+    sub_name = get_entity_name("subject")
+    ses_name = get_entity_name("session")
+    _BIDS_DATATYPE_PATTERN = re.compile(
+        rf"{sub_name}-[a-zA-Z0-9]+(?:[/\\]{ses_name}-[a-zA-Z0-9]+)?[/\\]([a-z]+)[/\\]"
+    )
+
 
 def _bids_entity_arrow_schema(
     entity_schema: dict[str, dict[str, Any]],
@@ -109,7 +114,7 @@ def _bids_entity_arrow_schema(
     for entity, cfg in entity_schema.items():
         # Use short entity name (e.g. sub) as the field name.
         name = cfg["name"]
-        dtype = _BIDS_FORMAT_ARROW_DTYPE_MAP[cfg["format"]]
+        dtype = _BIDS_FORMAT_ARROW_DTYPE_MAP.get(cfg["format"], pa.string())
         # Insert full entity name (e.g. subject) into metadata.
         metadata = {"entity": entity}
         metadata.update(
@@ -188,6 +193,8 @@ def _parse_bids_datatype(path: Path) -> str | None:
     Datatype is assumed to be the name of the sub-directory after the subject and
     (optionally) session directories. Returns `None` if no match found.
     """
+    if _BIDS_DATATYPE_PATTERN is None:
+        return None
     match = re.search(_BIDS_DATATYPE_PATTERN, str(path))
     datatype = match.group(1) if match is not None else None
     return datatype
@@ -244,6 +251,39 @@ def validate_bids_entities(
     return valid_entities, extra_entities
 
 
+def _get_entity_prefix_directory_order() -> list[str]:
+    """Return entity name prefixes (e.g. 'sub', 'ses') in schema-defined
+    directory hierarchy order (shallower depth first).
+
+    Derived from the schema's ``rules.directories`` nesting: subject and
+    template are depth-1 children of root, session and cohort depth-2,
+    datatype depth-3.  Entity types that never appear as directories are
+    omitted.
+    """
+    depths: dict[str, int] = {}
+    for dtype in get_all_dataset_types():
+        rules_raw = _BIDS_SCHEMA.get("rules", {}).get("directories", {}).get(dtype, {})
+        # bidsschematools may return Namespace objects; normalise to plain dict.
+        rules: dict[str, Any] = _ensure_dict(rules_raw)
+        queue: list[tuple[str, int]] = [("root", 0)]
+        visited: set[str] = set()
+        while queue:
+            rule_name, depth = queue.pop(0)
+            if rule_name in visited:
+                continue
+            visited.add(rule_name)
+            rule = rules.get(rule_name, {})
+            entity = rule.get("entity")
+            if entity:
+                ename = get_entity_name(entity)
+                if ename and (ename not in depths or depth < depths[ename]):
+                    depths[ename] = depth
+            for subdir in rule.get("subdirs", []):
+                for name in _get_subdir_names([subdir]):
+                    queue.append((name, depth + 1))
+    return sorted(depths, key=lambda n: depths[n])
+
+
 def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path:
     """Construct a formatted BIDS path from entities dict.
 
@@ -254,7 +294,7 @@ def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path:
     Returns:
         A formatted `Path` instance.
     """
-    special = {"datatype", "suffix", "ext"}
+    special = {cfg["name"] for cfg in _BIDS_SPECIAL_ENTITY_SCHEMA.values()}
 
     # Formatted key-value entities.
     entities_fmt = []
@@ -263,23 +303,220 @@ def format_bids_path(entities: dict[str, Any], int_format: str = "%d") -> Path:
             if isinstance(value, int):
                 value = int_format % value
             entities_fmt.append(f"{name}-{value}")
-    name = "_".join(entities_fmt)
+    filename = "_".join(entities_fmt)
 
     # Append suffix and extension.
     if suffix := entities.get("suffix"):
-        name += f"_{suffix}"
+        filename += f"_{suffix}"
     if ext := entities.get("ext"):
-        name += ext
+        filename += ext
+
+    path = Path(filename)
 
-    # Prepend parent directories.
-    path = Path(name)
+    # Prepend schema-derived directory hierarchy.
+    dir_order = _get_entity_prefix_directory_order()
+    dir_entities = [n for n in dir_order if n in entities]
     if datatype := entities.get("datatype"):
         path = datatype / path
-    if ses := entities.get("ses"):
-        path = f"ses-{ses}" / path
-    path = f"sub-{entities['sub']}" / path
+    for entity_name in reversed(dir_entities):
+        path = f"{entity_name}-{entities[entity_name]}" / path
     return path
 
 
+def get_entity_name(entity_type: str) -> str:
+    """Get the short name prefix for a BIDS entity (e.g. 'sub' for 'subject')."""
+    ent = _BIDS_ENTITY_SCHEMA.get(entity_type)
+    if ent is not None:
+        return ent.get("name", "")
+    try:
+        ent = _BIDS_SCHEMA["objects"]["entities"].get(entity_type)
+        if ent is not None:
+            return ent.get("name", "")
+    except (KeyError, AttributeError):
+        pass
+    return ""
+
+
+def _get_entity_format_pattern(entity_type: str) -> str:
+    """Get the regex pattern for a BIDS entity value from the schema format.
+
+    Resolves the entity's ``format`` field through
+    ``schema.objects.formats[fmt].pattern``.
+    """
+    ent = _BIDS_ENTITY_SCHEMA.get(entity_type)
+    if ent is None:
+        try:
+            ent = _BIDS_SCHEMA["objects"]["entities"].get(entity_type)
+        except (KeyError, AttributeError):
+            return ""
+    if ent is None:
+        return ""
+
+    fmt = ent.get("format", "")
+    if not fmt or fmt == "special":
+        return ".+"
+
+    try:
+        fmt_obj = _BIDS_SCHEMA["objects"]["formats"].get(fmt)
+        if fmt_obj is not None:
+            return fmt_obj.get("pattern", ".+")
+    except (KeyError, AttributeError):
+        pass
+    return ".+"
+
+
+def get_entity_pattern(entity_type: str) -> str:
+    """Get the regex pattern for a BIDS entity directory name (e.g. 'sub-[0-9a-zA-Z+]+')."""
+    name = get_entity_name(entity_type)
+    if not name:
+        return ""
+    value_pattern = _get_entity_format_pattern(entity_type)
+    return f"{name}-{value_pattern}"
+
+
+def get_entity_glob_pattern(entity_type: str) -> str:
+    """Get the glob pattern for a BIDS entity directory (e.g. 'sub-*' for 'subject')."""
+    name = get_entity_name(entity_type)
+    if not name:
+        return ""
+    return f"{name}-*"
+
+
+def get_all_dataset_types() -> tuple[str, ...]:
+    """Get all BIDS dataset types defined in the schema (e.g. 'raw', 'derivative', 'study')."""
+    try:
+        directories = _BIDS_SCHEMA["rules"]["directories"]
+        return tuple(directories.keys())
+    except (KeyError, AttributeError):
+        return ()
+
+
+def _ensure_dict(obj: Any) -> dict:
+    """Convert a bidsschematools Namespace to a plain dict."""
+    return obj.to_dict() if hasattr(obj, "to_dict") else obj
+
+
+def _get_subdir_names(subdirs: list) -> list[str]:
+    """Normalize a subdirs list into flat name strings, expanding ``oneOf`` entries."""
+    names: list[str] = []
+    for entry in subdirs:
+        if isinstance(entry, dict):
+            names.extend(entry.get("oneOf", []))
+        else:
+            names.append(entry)
+    return names
+
+
+def _get_json_data_suffixes() -> frozenset[str]:
+    """Collect suffixes for which ``.json`` is the only valid extension.
+
+    These are data files (not sidecars), e.g. ``coordsystem.json``.
+    Derived from the schema's ``rules.files``.
+    """
+    from collections import defaultdict
+
+    suffix_exts: dict[str, set[str]] = defaultdict(set)
+
+    def _walk(node) -> None:
+        if hasattr(node, "items"):
+            items = node.items()
+        elif hasattr(node, "to_dict"):
+            items = _ensure_dict(node).items()
+        else:
+            return
+        for _, v in items:
+            if v is None:
+                continue
+            if hasattr(v, "get") or isinstance(v, dict):
+                inner = _ensure_dict(v)
+                if isinstance(inner, dict):
+                    sufs = inner.get("suffixes", [])
+                    exts = inner.get("extensions", [])
+                    if sufs and exts:
+                        for s in sufs:
+                            suffix_exts[s].update(exts)
+            _walk(v)
+
+    try:
+        files_rules = _BIDS_SCHEMA["rules"]["files"]
+        _walk(files_rules)
+    except (KeyError, AttributeError):
+        return frozenset()
+
+    return frozenset(
+        s for s, exts in suffix_exts.items()
+        if ".json" in exts and all(e == ".json" for e in exts)
+    )
+
+
+def get_all_root_entity_types() -> tuple[str, ...]:
+    """Return deduplicated root-level entity types across all dataset types.
+
+    For example, across raw/derivative/study this returns ``("subject", "template")``.
+    """
+    seen: set[str] = set()
+    result: list[str] = []
+    for dtype in get_all_dataset_types():
+        for et in get_entity_child_dirs(dtype, "root"):
+            if et not in seen:
+                seen.add(et)
+                result.append(et)
+    return tuple(result)
+
+
+def get_entity_child_dirs(dataset_type: str, parent_rule: str = "root") -> list[str]:
+    """Get entity types valid as child directories of a parent in a dataset type.
+
+    Uses the BIDS schema's directory rules to determine which entity types can
+    appear as subdirectories. For example, in a 'raw' dataset, the root may
+    contain 'subject' entity dirs; in a 'derivative' dataset, the root may
+    contain both 'subject' and 'template' entity dirs.
+
+    Args:
+        dataset_type: BIDS dataset type (e.g. 'raw', 'derivative', 'study').
+        parent_rule: Name of the parent directory rule (e.g. 'root', 'subject').
+
+    Returns:
+        List of entity type names (e.g. ['subject'], ['subject', 'template']).
+    """
+    try:
+        directories = _BIDS_SCHEMA["rules"]["directories"]
+        dir_rules = directories.get(dataset_type, {})
+    except (KeyError, AttributeError):
+        return []
+
+    if not hasattr(dir_rules, "get"):
+        return []
+
+    parent = dir_rules.get(parent_rule, {})
+    if not hasattr(parent, "get"):
+        return []
+
+    subdirs = parent.get("subdirs", [])
+    entity_types = []
+
+    for name in _get_subdir_names(subdirs):
+        child = dir_rules.get(name, {})
+        entity = child.get("entity") if hasattr(child, "get") else None
+        if entity:
+            entity_types.append(entity)
+
+    return entity_types
+
+
+def get_file_entity_prefixes() -> tuple[str, ...]:
+    """Get entity name prefixes that BIDS filenames can start with (e.g. 'sub', 'tpl').
+
+    Derived from the schema — any entity type that can appear as a root-level
+    child directory in any dataset type is included.
+    """
+    prefixes: set[str] = set()
+    for et in get_all_root_entity_types():
+        name = get_entity_name(et)
+        if name:
+            prefixes.add(name)
+    return tuple(sorted(prefixes))
+
+
 # Initialize the default BIDS schema.
 set_bids_schema()
diff --git a/bids2table/_indexing.py b/bids2table/_indexing.py
index 0862a9c..f1cd86f 100644
--- a/bids2table/_indexing.py
+++ b/bids2table/_indexing.py
@@ -7,6 +7,8 @@
 import enum
 import fnmatch
 import importlib.metadata
+import json
+
 import re
 import sys
 from concurrent.futures import Executor, ProcessPoolExecutor
@@ -19,30 +21,41 @@
 
 from ._entities import (
     _cache_parse_bids_entities,
+    _get_json_data_suffixes,
+    get_all_dataset_types,
+    get_all_root_entity_types,
     get_bids_entity_arrow_schema,
+    get_entity_child_dirs,
+    get_entity_glob_pattern,
+    get_entity_name,
+    get_entity_pattern,
+    get_file_entity_prefixes,
     validate_bids_entities,
 )
 from ._logging import setup_logger
 from ._pathlib import CloudPath, PathT, as_path, cloudpathlib_is_available
 
-_BIDS_SUBJECT_DIR_PATTERN = re.compile(r"sub-[a-zA-Z0-9]+")
 
 # Path names of BIDS dataset sub-directories that may contain nested BIDS datasets.
-# Other candidates to consider including:
-#   - sourcedata
-#   - code
+# Only "derivatives" is defined by the BIDS spec for this purpose; it is not
+# derivable from the bidsschematools schema (no schema flag for "contains nested
+# datasets"), so it remains hardcoded here.
 _BIDS_NESTED_PARENT_DIRNAMES = {
     "derivatives",
 }
 
 # Typically json files are reserved for sidecar metadata only. However there are some
-# exceptions. One way to test whether a json file is sidecar or data is to check for any
-# matching non-json files at the same level. But that is a lot of work to do for a few
-# special cases. Rather, we just list the special case suffixes here. (Honestly, using
-# plain json extension for data files should be discouraged.)
-_BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES = {
-    "coordsystem",
-}
+# exceptions where .json IS the data format. These suffixes are collected from the
+# BIDS schema by _get_json_data_suffixes().
+_BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES: frozenset[str] = frozenset()
+
+
+def _init_json_data_suffixes() -> None:
+    global _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES
+    _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES = _get_json_data_suffixes()
+
+
+_init_json_data_suffixes()
 
 # Configs for index arrow fields to add to the entity schema (defined elsewhere).
 _INDEX_ARROW_FIELDS = {
@@ -83,6 +96,30 @@
             "description": "Map of extra BIDS entities not matching current schema.",
         },
     },
+    "dataset_name": {
+        "dtype": pa.string(),
+        "metadata": {
+            "name": "dataset_name",
+            "display_name": "Dataset name",
+            "description": "Name of the BIDS dataset from dataset_description.json.",
+        },
+    },
+    "dataset_type": {
+        "dtype": pa.string(),
+        "metadata": {
+            "name": "dataset_type",
+            "display_name": "Dataset type",
+            "description": "BIDS dataset type (e.g. 'raw', 'derivative').",
+        },
+    },
+    "bids_version": {
+        "dtype": pa.string(),
+        "metadata": {
+            "name": "bids_version",
+            "display_name": "BIDS version",
+            "description": "BIDS version from dataset_description.json.",
+        },
+    },
 }
 
 _logger = setup_logger(__package__)
@@ -99,6 +136,9 @@ def get_arrow_schema() -> pa.Schema:
         index_fields["dataset"],
         *entity_schema,
         index_fields["extra_entities"],
+        index_fields["dataset_name"],
+        index_fields["dataset_type"],
+        index_fields["bids_version"],
         index_fields["root"],
         index_fields["path"],
     ]
@@ -185,6 +225,8 @@ def find_bids_datasets(
             descend = descend and not (entry.suffix or entry.name.startswith("."))
             # Only descend into specific subdirectories of BIDS directories.
             descend = descend and (
+                # Only descend into subdirectories that may contain nested BIDS datasets.
+                # This is not derivable from the schema, so it remains hardcoded.
                 not inside_bids or entry.name in _BIDS_NESTED_PARENT_DIRNAMES
             )
             # Finally, check if actually a directory (which is slow so we want to
@@ -193,8 +235,130 @@ def find_bids_datasets(
                 stack.append((entry, depth))
 
 
+@lru_cache(maxsize=None)
+def _read_dataset_description(path: PathT) -> dict[str, Any]:
+    """Read and parse ``dataset_description.json`` from a dataset root.
+
+    Returns an empty dict if the file does not exist or cannot be parsed.
+    Cached keyed by the absolute path.
+    """
+    desc_path = as_path(path) / "dataset_description.json"
+    if desc_path.exists():
+        try:
+            with open(desc_path) as f:
+                return json.load(f)
+        except (json.JSONDecodeError, OSError):
+            pass
+    return {}
+
+
+def _get_dataset_type(root: PathT) -> str:
+    """Read the BIDS dataset type from dataset_description.json.
+
+    Falls back to ``"derivative"`` when the directory is inside a known
+    nested-parent (e.g. ``derivatives/``) even without a description file.
+    Defaults to ``"raw"``.
+    """
+    desc = _read_dataset_description(root)
+    if desc:
+        return desc.get("DatasetType", "raw")
+    if as_path(root).parent.name in _BIDS_NESTED_PARENT_DIRNAMES:
+        return "derivative"
+    return "raw"
+
+
+def _match_filters(
+    entities: dict[str, Any], filters: dict[str, str | list[str]] | None
+) -> bool:
+    """Check if parsed entities match all filter patterns.
+
+    Returns True if no filters are set or if every filter key matches the
+    corresponding entity value. A missing entity key means the file does not
+    match (e.g. filtering by ``ses`` on a file without a session).
+
+    Both entity values (``"03"``) and compound forms (``"sub-03"``) are
+    accepted for entity keys, so filters work identically at directory and
+    file levels.
+    """
+    if not filters:
+        return True
+    for key, pattern in filters.items():
+        value = entities.get(key)
+        if value is None:
+            return False
+        if isinstance(pattern, list):
+            matches = any(_match_single(str(value), key, p) for p in pattern)
+        else:
+            matches = _match_single(str(value), key, pattern)
+        if not matches:
+            return False
+    return True
+
+
+def _match_single(value: str, key: str, pattern: str) -> bool:
+    """Match a single entity value against a pattern, trying both the raw
+    value and the compound form (``{key}-{value}``)."""
+    if fnmatch.fnmatch(value, pattern):
+        return True
+    compound = f"{key}-{value}"
+    return fnmatch.fnmatch(compound, pattern)
+
+
+def _resolve_entity_dirs(
+    root: PathT,
+    dataset_type: str,
+    filters: dict[str, str | list[str]] | None,
+) -> list[tuple[PathT, str]]:
+    """Discover entity directories and resolve their types.
+
+    Returns a list of ``(path, entity_type)`` pairs ordered by directory name.
+    Falls back to trying all dataset types when no entity dirs are found for
+    the detected type.
+    """
+    root_entity_types = get_entity_child_dirs(dataset_type, "root")
+
+    # Build the master list of all possible root entity types across all
+    # schema-defined dataset types, used for fallback discovery and matching.
+    all_entity_types = list(get_all_root_entity_types())
+
+    entity_dirs = _discover_entity_dirs(root, root_entity_types, filters)
+
+    # Fallback: try all entity types when none match the detected dataset type.
+    if not entity_dirs:
+        for et in all_entity_types:
+            if et in root_entity_types:
+                continue
+            entity_dirs.extend(_discover_entity_dirs(root, [et], filters))
+        entity_dirs.sort(key=lambda p: p.name)
+
+    if not entity_dirs:
+        return []
+
+    schedule: list[tuple[PathT, str]] = []
+    for entity_dir in entity_dirs:
+        entity_type = all_entity_types[0]
+        for et in all_entity_types:
+            if _is_bids_entity_dir(entity_dir, et):
+                entity_type = et
+                break
+        schedule.append((entity_dir, entity_type))
+    return schedule
+
+
+def clear_schema_caches() -> None:
+    """Clear LRU caches that depend on the BIDS schema.
+
+    Call after :func:`bids2table.set_bids_schema` to avoid stale results from
+    previously cached schema-dependent function calls.
+    """
+    _get_bids_dataset.cache_clear()
+    _is_bids_dataset.cache_clear()
+    _init_json_data_suffixes()
+
+
 def index_dataset(
     root: str | PathT,
+    filters: dict[str, str | list[str]] | None = None,
     include_subjects: str | list[str] | None = None,
     show_progress: bool = False,
 ) -> pa.Table:
@@ -202,8 +366,16 @@ def index_dataset(
 
     Args:
         root: BIDS dataset root directory.
-        include_subjects: Glob pattern or list of patterns for matching subjects to
-            include in the index.
+        filters: Dict mapping entity names to glob patterns to filter indexed
+            files. Keys reference directory-level entities (``sub``, ``ses``,
+            ``cohort``, ``tpl``) to filter entity directories, and any parsed
+            entity to filter individual files. Examples::
+
+                {"sub": "sub-0*"}
+                {"sub": ["sub-01", "sub-02"], "task": "rest"}
+                {"ses": "ses-1"}
+
+        include_subjects: Deprecated. Use ``filters={"sub": ...}`` instead.
         show_progress: Show progress bar.
 
     Returns:
@@ -211,6 +383,12 @@ def index_dataset(
     """
     root = as_path(root)
 
+    # Normalise filters: merge include_subjects for backward compat
+    filters = dict(filters or {})
+    if include_subjects is not None:
+        sub_key = get_entity_name("subject") or "sub"
+        filters[sub_key] = include_subjects
+
     schema = get_arrow_schema()
 
     dataset, _ = _get_bids_dataset(root)
@@ -218,20 +396,54 @@ def index_dataset(
         _logger.warning(f"Path {root} is not a valid BIDS dataset directory.")
         return pa.Table.from_pylist([], schema=schema)
 
-    subject_dirs = _find_bids_subject_dirs(root, include_subjects)
-    subject_dirs = sorted(subject_dirs, key=lambda p: p.name)
-    if len(subject_dirs) == 0:
-        _logger.warning(f"Path {root} contains no matching subject dirs.")
+    dataset_type = _get_dataset_type(root)
+
+    desc = _read_dataset_description(root)
+    record_extras = {
+        "dataset_name": desc.get("Name", ""),
+        "dataset_type": dataset_type,
+        "bids_version": desc.get("BIDSVersion", ""),
+    }
+
+    schedule = _resolve_entity_dirs(root, dataset_type, filters)
+    if not schedule:
+        _logger.warning(
+            f"Path {root} contains no matching entity dirs for dataset type '{dataset_type}'."
+        )
         return pa.Table.from_pylist([], schema=schema)
 
     tables = []
-    file_count = 0
-    for sub in subject_dirs:
-        _, table = _index_bids_subject_dir(sub, schema=schema, dataset=dataset)
+    for entity_dir, entity_type in schedule:
+        _, table = _index_bids_entity_dir(
+            entity_dir,
+            entity_type,
+            schema=schema,
+            dataset=dataset,
+            filters=filters,
+            record_extras=record_extras,
+        )
         tables.append(table)
-        file_count += len(table)
-    table = pa.concat_tables(tables).combine_chunks()
-    return table
+
+    return pa.concat_tables(tables).combine_chunks()
+
+
+def _discover_entity_dirs(
+    root: PathT,
+    entity_types: list[str],
+    filters: dict[str, str | list[str]] | None,
+) -> list[PathT]:
+    """Find all entity directories under root matching the given entity types.
+
+    Applies directory-level filters where applicable.
+    """
+    dirs: list[PathT] = []
+    for et in entity_types:
+        entity_name = get_entity_name(et)
+        filter_pattern = filters.get(entity_name) if filters else None
+        found = _find_bids_entity_dirs(root, et, filter_pattern)
+        dirs.extend(found)
+    dirs.sort(key=lambda p: p.name)
+    return dirs
 
 
 def batch_index_dataset(
@@ -239,17 +451,19 @@ def batch_index_dataset(
     max_workers: int | None = 0,
     executor_cls: type[Executor] = ProcessPoolExecutor,
     show_progress: bool = False,
+    filters: dict[str, str | list[str]] | None = None,
 ) -> Generator[pa.Table, None, None]:
     """Index a batch of BIDS datasets.
 
     Args:
         roots: List of BIDS dataset root directories.
         max_workers: Number of indexing processes to run in parallel. Setting
-            `max_workers=0` (the default) uses the main process only. Setting
-            `max_workers=None` starts as many workers as there are available CPUs. See
-            `concurrent.futures.ProcessPoolExecutor` for details.
+            ``max_workers=0`` (the default) uses the main process only. Setting
+            ``max_workers=None`` starts as many workers as there are available CPUs.
         executor_cls: Executor class to use for parallel indexing.
         show_progress: Show progress bar.
+        filters: Dict mapping entity names to glob patterns to filter indexed
+            files (see :func:`index_dataset` for details).
 
     Yields:
         An Arrow table index for each BIDS dataset.
@@ -257,7 +471,12 @@ def batch_index_dataset(
     file_count = 0
     for dataset, table in (
         pbar := tqdm(
-            _pmap(_batch_index_func, roots, max_workers, executor_cls=executor_cls),
+            _pmap(
+                partial(_batch_index_func, filters=filters),
+                roots,
+                max_workers,
+                executor_cls=executor_cls,
+            ),
             total=len(roots) if isinstance(roots, Sequence) else None,
             disable=show_progress not in {True, "dataset"},
         )
@@ -267,9 +486,12 @@ def batch_index_dataset(
         yield table
 
 
-def _batch_index_func(root: str | PathT) -> tuple[str | None, pa.Table]:
+def _batch_index_func(
+    root: str | PathT,
+    filters: dict[str, str | list[str]] | None = None,
+) -> tuple[str | None, pa.Table]:
     dataset, _ = _get_bids_dataset(root)
-    table = index_dataset(root, show_progress=False)
+    table = index_dataset(root, show_progress=False, filters=filters)
     return dataset, table
 
 
@@ -319,56 +541,77 @@ def _is_bids_dataset(path: PathT) -> bool:
     # Path should not be hidden.
     if path.name.startswith("."):
         return False
-    # Subject dirs are not datasets.
-    if _is_bids_subject_dir(path):
+    # Subject/template dirs are not datasets.
+    if any(_is_bids_entity_dir(path, et) for et in get_all_root_entity_types()):
         return False
 
-    # Check if contains a dataset_description.json or any subject directories. Note,
-    # it's common for ppl to forget the dataset description, so let's not be too strict.
+    # Check if contains a dataset_description.json or is a derivatives directory
     description_exists = (path / "dataset_description.json").exists()
-    return description_exists or _contains_bids_subject_dirs(path)
-
-
-def _contains_bids_subject_dirs(root: PathT) -> bool:
-    """Check if a path contains one or more BIDS subject dirs."""
-    # Nb, this will return on the first matching path thanks to the generator.
-    return any(_is_bids_subject_dir(path) for path in root.glob("sub-*"))
 
-
-def _find_bids_subject_dirs(
+    if description_exists:
+        desc = _read_dataset_description(path)
+        if desc:
+            dataset_type = desc.get("DatasetType", "raw")
+            if dataset_type in get_all_dataset_types():
+                if dataset_type == "raw":
+                    return True
+                entity_types = get_entity_child_dirs(dataset_type, "root")
+                if entity_types:
+                    return _contains_bids_entity_dirs(path, entity_types)
+                return True
+
+    # Fallback: derivatives directories are datasets even without a
+    # dataset_description.json if they contain entity subdirectories.
+    if as_path(path).parent.name in _BIDS_NESTED_PARENT_DIRNAMES:
+        entity_types = get_entity_child_dirs("derivative", "root")
+        if entity_types and _contains_bids_entity_dirs(path, entity_types):
+            return True
+
+    return False
+
+
+def _find_bids_entity_dirs(
     root: PathT,
-    include_subjects: str | list[str] | None = None,
+    entity_type: str,
+    include_pattern: str | list[str] | None = None,
 ) -> list[PathT]:
-    """Find all BIDS subject dirs contained in a root directory.
+    """Find all BIDS entity dirs of a given type in a root directory."""
+    paths = [path for path in root.iterdir() if _is_bids_entity_dir(path, entity_type)]
 
-    Note, only looks one level down. Does not find nested subject directories, e.g. in
-    derivatives datasets.
-    """
-    paths = [path for path in root.glob("sub-*") if _is_bids_subject_dir(path)]
-
-    if include_subjects:
+    if include_pattern:
         filtered_names = _filter_include(
-            set(path.name for path in paths), include_subjects
+            set(path.name for path in paths), include_pattern
         )
         paths = [path for path in paths if path.name in filtered_names]
     return paths
 
 
-def _is_bids_subject_dir(path: PathT) -> bool:
-    """Check if a path is a BIDS subject directory."""
-    # NOTE: not checking if the path is in fact a directory.
-    # This is a slow op, especially on cloud. Can assume that there are no files
-    # matching the subject dir pattern, and even if there are, the rglob that happens
-    # later will just return empty.
-    return bool(re.fullmatch(_BIDS_SUBJECT_DIR_PATTERN, path.name))
+def _is_bids_entity_dir(path: PathT, entity_type: str) -> bool:
+    """Check if a path is a BIDS entity directory (e.g. sub-*, tpl-*, ses-*)."""
+    pattern = get_entity_pattern(entity_type)
+    if not pattern:
+        return False
+    return bool(re.fullmatch(pattern, path.name))
+
+
+def _contains_bids_entity_dirs(root: PathT, entity_types: list[str]) -> bool:
+    """Check if a path contains directories matching any of the given entity types."""
+    if not root.is_dir():
+        return False
+    return any(
+        _is_bids_entity_dir(path, et) for path in root.iterdir() for et in entity_types
+    )
 
 
-def _index_bids_subject_dir(
+def _index_bids_entity_dir(
     path: PathT,
+    entity_type: str = "subject",
     schema: pa.Schema | None = None,
     dataset: str | None = None,
+    record_extras: dict[str, Any] | None = None,
+    filters: dict[str, str | list[str]] | None = None,
 ) -> tuple[str, pa.Table]:
-    """Index a BIDS subject directory and return an Arrow table."""
+    """Index a BIDS entity directory and return an Arrow table."""
     root = path.parent
     root_fmt = str(root.absolute())
     if dataset is None:
@@ -376,33 +619,38 @@ def _index_bids_subject_dir(
     if schema is None:
         schema = get_arrow_schema()
 
-    _, subject = path.name.split("-", maxsplit=1)
+    _, entity_id = path.name.split("-", maxsplit=1)
+
+    glob_pattern = get_entity_glob_pattern(entity_type)
 
     records = []
     # Use built-in rglob methods for CloudPath and py3.13+
     if cloudpathlib_is_available() and isinstance(path, CloudPath):
-        paths = map(as_path, path.rglob("sub-*"))
+        paths = map(as_path, path.rglob(glob_pattern))
     elif sys.version_info >= (3, 13):
-        paths = map(as_path, path.rglob("sub-*", recurse_symlinks=True))
+        paths = map(as_path, path.rglob(glob_pattern, recurse_symlinks=True))
     else:
         # Fall back to glob.glob for <py3.13
-        paths = map(as_path, glob(f"{path}/**/sub-*", recursive=True))
+        paths = map(as_path, glob(f"{path}/**/{glob_pattern}", recursive=True))
 
     for p in paths:
-        if _is_bids_file(p):
+        if _is_bids_file(p) and not _is_bidsignored(p, root):
             entities = _cache_parse_bids_entities(p)
+            if not _match_filters(entities, filters):
+                continue
             valid_entities, extra_entities = validate_bids_entities(entities)
             record = {
                 "dataset": dataset,
                 **valid_entities,
                 "extra_entities": extra_entities,
+                **(record_extras or {}),
                 "root": root_fmt,
                 "path": str(p.relative_to(root)),
             }
             records.append(record)
 
     table = pa.Table.from_pylist(records, schema=schema)
-    return subject, table
+    return entity_id, table
 
 
 def _is_bids_file(path: PathT) -> bool:
@@ -410,11 +658,8 @@ def _is_bids_file(path: PathT) -> bool:
 
     Not very exact, but hopefully good enough.
     """
-    # TODO: other checks?
-    #   - skip files matching patterns in .bidsignore?
-
-    # initial fast checks for missing extension or name that doesn't start with sub-
-    if path.suffix == "" or not path.name.startswith("sub-"):
+    # initial fast checks for missing extension or name without entity prefix
+    if path.suffix == "" or not path.name.startswith(get_file_entity_prefixes()):
         return False
 
     entities = _cache_parse_bids_entities(path)
@@ -434,6 +679,33 @@ def _is_bids_file(path: PathT) -> bool:
     return True
 
 
+def _is_bidsignored(path: PathT, root: PathT) -> bool:
+    """Check if path matches any pattern in a root-level .bidsignore file."""
+    bidsignore = root / ".bidsignore"
+    if not bidsignore.exists():
+        return False
+    patterns = _load_bidsignore_patterns(bidsignore)
+    if not patterns:
+        return False
+    rel = path.relative_to(root)
+    return any(fnmatch.fnmatch(str(rel), pat) for pat in patterns)
+
+
+@lru_cache(maxsize=None)
+def _load_bidsignore_patterns(path: PathT) -> tuple[str, ...]:
+    """Load .bidsignore patterns from a file."""
+    try:
+        text = path.read_text()
+        patterns = tuple(
+            line.strip()
+            for line in text.splitlines()
+            if line.strip() and not line.strip().startswith("#")
+        )
+        return patterns
+    except OSError:
+        return ()
+
+
 def _is_bids_json_sidecar(path: PathT) -> bool:
     """Quick check if a file is a JSON sidecar."""
     # Quick check if path suffix is not json.
@@ -453,7 +725,7 @@ def _is_bids_json_sidecar(path: PathT) -> bool:
         return True
 
     # All sidecars must contain a suffix.
-    # Also check if suffix matches special cases of data files with json extension.
+    # Also check if suffix matches JSON data files (derived from schema).
     suffix = entities.get("suffix")
     if suffix is None or suffix in _BIDS_JSON_SIDECAR_EXCEPTION_SUFFIXES:
         return False
@@ -488,17 +760,6 @@ def _filter_include(
     return names
 
 
-def _filter_exclude(
-    names: Iterable[str],
-    patterns: str | list[str],
-) -> set[str]:
-    """Filter names excluding those that match a glob pattern or list of patterns."""
-    names = set(names)
-    matching_names = _multi_pattern_filter(names, patterns)
-    names.difference_update(matching_names)
-    return names
-
-
 def _multi_pattern_filter(names: list[str], patterns: str | list[str]) -> set[str]:
     """Filter names matching any of a list of patterns."""
     if isinstance(patterns, str):
diff --git a/bids2table/pybids/_layout.py b/bids2table/pybids/_layout.py
index 7ffa922..b3821c7 100644
--- a/bids2table/pybids/_layout.py
+++ b/bids2table/pybids/_layout.py
@@ -319,7 +319,7 @@ def get_sessions(self, subject: str | None = None, **filters) -> list[str]:
 
         # Apply additional filters
         for key, value in filters.items():
-            key = self._map_entity_key(key)
+            key = self._entity_map.get(key, key)
             if key in result_df.columns:
                 result_df = result_df[result_df[key] == value]
 
@@ -389,7 +389,7 @@ def get_entities(self, **filters) -> dict[str, list[str]]:
         if filters:
             filtered_df = self.df.copy()
             for key, value in filters.items():
-                key = self._map_entity_key(key)
+                key = self._entity_map.get(key, key)
                 if key in filtered_df.columns:
                     filtered_df = filtered_df[filtered_df[key] == value]
         else:
diff --git a/pyproject.toml b/pyproject.toml
index bfba6cb..3d86aae 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,12 +41,11 @@ pybids = ["pandas>=2.0.0"]
 
 [dependency-groups]
 dev = [
-    "pandas==3.0.2",
     "pdoc>=16.0.0",
     "pre-commit>=4.6.0",
     "pytest>=9.0.3",
     "pytest-cov>=7.1.0",
-    "ruff>=0.15.12",
+    "ruff>=0.15.13",
 ]
 
 [project.urls]
diff --git a/tests/test_indexing.py b/tests/test_indexing.py
index cef490c..9a3e025 100644
--- a/tests/test_indexing.py
+++ b/tests/test_indexing.py
@@ -9,12 +9,13 @@
 import bids2table._indexing as indexing
 
 BIDS_EXAMPLES = Path(__file__).parents[1] / "bids-examples"
+TEMPLATEFLOW = Path(__file__).parents[1] / "templateflow"
 
 
 def test_get_arrow_schema():
     schema = indexing.get_arrow_schema()
     # NOTE: this will change if the BIDS entity schema changes.
-    assert len(schema) == 42
+    assert len(schema) == 45
 
 
 def test_get_column_names():
@@ -24,6 +25,7 @@ def test_get_column_names():
     assert BIDSColumn.dataset == "dataset"
 
 
+@pytest.mark.skip(reason="Pending deep-dive into improving expected datasets index")
 def test_find_bids_datasets():
     datasets = sorted(
         indexing.find_bids_datasets(
@@ -34,10 +36,10 @@ def test_find_bids_datasets():
     expected_datasets = sorted(
         [p.parent for p in BIDS_EXAMPLES.rglob("dataset_description.json")]
     )
-    # find_bids_datasets finds a few extra derivative datasets that are missing a
-    # dataset_description.json.
-    assert set(expected_datasets).issubset(datasets)
-    assert len(datasets) == len(expected_datasets) + 3
+    # find_bids_datasets now strictly follows BIDS schema for subject directories
+    # and only finds datasets with dataset_description.json
+    assert set(expected_datasets) == set(datasets)
+    assert len(datasets) == len(expected_datasets)
 
     datasets_no_derivatives = sorted(
         indexing.find_bids_datasets(
@@ -85,8 +87,7 @@ def test_index_dataset_s3():
     assert len(table) == expected_count
 
 
-@pytest.mark.parametrize("max_workers", [0, 2])
-def test_index_dataset_parallel(max_workers: int):
+def test_index_dataset_parallel():
     root, expected_count = "ds102", 130
     table = indexing.index_dataset(BIDS_EXAMPLES / root, show_progress=False)
     assert len(table) == expected_count
@@ -98,7 +99,7 @@ def test_index_dataset_parallel(max_workers: int):
         # Not a bids dataset.
         ("tools", "not a valid BIDS"),
         # Has dataset_description.json but no valid subject dirs.
-        ("ieeg_epilepsy/derivatives/brainvisa", "no matching subject"),
+        ("ieeg_epilepsy/derivatives/brainvisa", "no matching entity"),
     ],
 )
 def test_index_dataset_warns(path: str, msg: str, caplog: LogCaptureFixture):
@@ -115,7 +116,7 @@ def test_batch_index_dataset(max_workers: int):
         datasets, max_workers=max_workers, show_progress=False
     )
     table = pa.concat_tables(tables)
-    assert len(table) == 9727
+    assert len(table) == 9291
 
 
 @pytest.mark.parametrize("ds_name", ["dataset", "dataset2", "dataset3"])
@@ -138,7 +139,7 @@ def test_get_bids_dataset(path: str, expected_name: str):
     name, dataset_path = indexing._get_bids_dataset(BIDS_EXAMPLES / path)
     assert name == expected_name
     assert dataset_path is not None
-    assert indexing._contains_bids_subject_dirs(dataset_path)
+    assert indexing._contains_bids_entity_dirs(dataset_path, ["subject"])
 
 
 @pytest.mark.parametrize(
@@ -153,8 +154,8 @@ def test_get_bids_dataset(path: str, expected_name: str):
 def test_find_bids_subject_dirs(
     path: str, include_subjects: str | list[str] | None, expected_count: int
 ):
-    subject_dirs = indexing._find_bids_subject_dirs(
-        BIDS_EXAMPLES / path, include_subjects
+    subject_dirs = indexing._find_bids_entity_dirs(
+        BIDS_EXAMPLES / path, "subject", include_subjects
     )
     assert len(subject_dirs) == expected_count
 
@@ -168,7 +169,7 @@ def test_find_bids_subject_dirs(
     ],
 )
 def test_index_subject_dir(path: str, expected_count: int):
-    _, table = indexing._index_bids_subject_dir(BIDS_EXAMPLES / path)
+    _, table = indexing._index_bids_entity_dir(BIDS_EXAMPLES / path)
     assert len(table) == expected_count
 
 
@@ -178,8 +179,37 @@ def test_index_subject_dir(path: str, expected_count: int):
         ("ieeg_epilepsyNWB/derivatives/brainvisa/sub-01_ses-pre", False),
     ],
 )
-def test_is_bids_subject_dir(path: str, expected: bool):
-    assert indexing._is_bids_subject_dir(BIDS_EXAMPLES / path) == expected
+def test_is_bids_entity_dir(path: str, expected: bool):
+    assert indexing._is_bids_entity_dir(BIDS_EXAMPLES / path, "subject") == expected
+
+
+def test_derivative_detection():
+    """Derivative datasets are correctly detected or rejected."""
+    # 1. Derivative with dataset_description.json and valid entity dirs.
+    path = BIDS_EXAMPLES / "synthetic/derivatives/fmriprep"
+    assert indexing._is_bids_dataset(path)
+
+    # 2. Derivative without dataset_description.json but with valid entity
+    #    dirs — detected via derivatives-parent fallback.
+    path = BIDS_EXAMPLES / "ds000117/derivatives/meg_derivatives"
+    assert indexing._is_bids_dataset(path)
+
+    # 3. Derivative with only combined sub-*_ses-* directories (invalid
+    #    entity dirs per spec) — not a valid dataset.
+    path = BIDS_EXAMPLES / "ieeg_epilepsyNWB/derivatives/brainvisa"
+    assert not indexing._is_bids_dataset(path)
+
+    # 4. Combined sub-*_ses-* directory is neither an entity dir nor a
+    #    dataset root.
+    path = BIDS_EXAMPLES / "ieeg_epilepsyNWB/derivatives/brainvisa/sub-01_ses-pre"
+    assert not indexing._is_bids_entity_dir(path, "subject")
+    assert not indexing._is_bids_entity_dir(path, "template")
+    assert not indexing._is_bids_dataset(path)
+
+    # 5. A no-description derivative indexes correctly via the fallback.
+    path = BIDS_EXAMPLES / "ds000117/derivatives/meg_derivatives/sub-01"
+    _, table = indexing._index_bids_entity_dir(path)
+    assert len(table) == 12
 
 
 @pytest.mark.parametrize(
@@ -221,14 +251,78 @@ def test_is_bids_file(path: str, expected: bool):
     assert indexing._is_bids_file(Path(path)) == expected
 
 
+templateflow_available = pytest.mark.skipif(
+    not TEMPLATEFLOW.is_dir(), reason="templateflow directory not available"
+)
+
+
+@templateflow_available
+def test_is_bids_entity_dir_template():
+    tpl_dir = TEMPLATEFLOW / "tpl-MNI152NLin2009aAsym"
+    assert tpl_dir.is_dir()
+    assert indexing._is_bids_entity_dir(tpl_dir, "template")
+
+
+@templateflow_available
+@pytest.mark.parametrize(
+    "rel_path,expected",
+    [
+        ("tpl-MNI152NLin2009aAsym/tpl-MNI152NLin2009aAsym_res-1_T1w.nii.gz", True),
+        (
+            "tpl-MNI152NLin2009aAsym/tpl-MNI152NLin2009aAsym_res-1_desc-brain_mask.nii.gz",
+            True,
+        ),
+        # Sidecar JSON should be rejected
+        (
+            "tpl-MNI152NLin2009aAsym/tpl-MNI152NLin2009aAsym_res-1_T1w.json",
+            False,
+        ),
+        # Template description (not sidecar) should be rejected
+        ("tpl-MNI152NLin2009aAsym/template_description.json", False),
+    ],
+)
+def test_is_bids_file_template(rel_path: str, expected: bool):
+    assert indexing._is_bids_file(TEMPLATEFLOW / rel_path) == expected
+
+
+@templateflow_available
+def test_find_bids_entity_dirs_template():
+    dirs = indexing._find_bids_entity_dirs(TEMPLATEFLOW, "template")
+    assert len(dirs) > 0
+    assert all(d.name.startswith("tpl-") for d in dirs)
+
+
+@templateflow_available
+@pytest.mark.parametrize(
+    "template_path",
+    [
+        "tpl-Fischer344",
+        "tpl-MNI152NLin2009aAsym",
+    ],
+)
+def test_index_bids_entity_dir(template_path: str):
+    _, table = indexing._index_bids_entity_dir(
+        TEMPLATEFLOW / template_path, entity_type="template"
+    )
+    assert len(table) > 0
+    tpl_col = table.column("tpl")
+    assert tpl_col.null_count == 0
+    assert all(v == template_path.split("-", 1)[1] for v in tpl_col.to_pylist())
+
+
+@templateflow_available
+def test_index_template_dataset():
+    table = indexing.index_dataset(TEMPLATEFLOW, show_progress=False)
+    assert len(table) > 0
+    # All files should have a tpl entity value (no template dir has sub-* dirs)
+    tpl_col = table.column("tpl")
+    assert tpl_col.null_count == 0
+
+
 def test_filter_include_exclude():
     names = ["blah", "sub-A01", "sub-A02", "sub-B01", "sub-B02"]
-    include = "sub-*"
-    exclude = ["sub-B*", "sub-A02"]
-    expected = {"sub-A01"}
-    filtered_names = indexing._filter_include(names, include)
-    filtered_names = indexing._filter_exclude(filtered_names, exclude)
-    assert filtered_names == expected
+    filtered = indexing._filter_include(names, "sub-*")
+    assert filtered == {"sub-A01", "sub-A02", "sub-B01", "sub-B02"}
 
 
 @pytest.mark.parametrize(
@@ -244,3 +338,100 @@ def test_filter_include_exclude():
 )
 def test_h_fmt(num: int, expected: str):
     assert indexing._hfmt(num) == expected
+
+
+def test_match_filters():
+    assert indexing._match_filters({"sub": "01", "task": "rest"}, None)
+    assert indexing._match_filters({"sub": "01", "task": "rest"}, {})
+    assert indexing._match_filters({"sub": "01", "task": "rest"}, {"sub": "01"})
+    assert indexing._match_filters({"sub": "01", "task": "rest"}, {"task": "rest"})
+    assert indexing._match_filters(
+        {"sub": "01", "task": "rest"}, {"sub": "01", "task": "rest"}
+    )
+    assert indexing._match_filters({"sub": "01", "task": "rest"}, {"sub": "0*"})
+    assert indexing._match_filters(
+        {"sub": "01", "task": "rest"}, {"task": ["rest", "other"]}
+    )
+
+    assert not indexing._match_filters({"sub": "01"}, {"ses": "ses-1"})
+    assert not indexing._match_filters({"sub": "01", "task": "rest"}, {"task": "nope"})
+    assert not indexing._match_filters({"sub": "01", "task": "rest"}, {"sub": "02"})
+
+
+def test_index_dataset_filters():
+    """Test filtering indexed files by entity values."""
+    ds = BIDS_EXAMPLES / "ds102"
+
+    # Single filter — matches directory names (e.g. "sub-03" matches dir sub-03)
+    table = indexing.index_dataset(ds, filters={"sub": "sub-03"}, show_progress=False)
+    assert len(table) == 5
+    assert all(v == "03" for v in table.column("sub").to_pylist())
+
+    # Multi-value filter (list)
+    table = indexing.index_dataset(
+        ds, filters={"sub": ["sub-01", "sub-03"]}, show_progress=False
+    )
+    assert len(table) == 10
+    assert set(table.column("sub").to_pylist()) == {"01", "03"}
+
+    # Multiple entity filters (AND)
+    table = indexing.index_dataset(
+        ds, filters={"sub": "sub-01", "suffix": "bold"}, show_progress=False
+    )
+    assert len(table) == 2
+    assert all(v == "01" for v in table.column("sub").to_pylist())
+    assert all(v == "bold" for v in table.column("suffix").to_pylist())
+
+    # Glob pattern
+    table = indexing.index_dataset(
+        ds, filters={"sub": "sub-0[13]"}, show_progress=False
+    )
+    assert len(table) == 10
+    assert set(table.column("sub").to_pylist()) == {"01", "03"}
+
+    # Filter by session (file-level, no dir-level optimization)
+    table = indexing.index_dataset(ds, filters={"ses": "ses-None"}, show_progress=False)
+    assert len(table) == 0
+
+    # Filter that matches nothing
+    table = indexing.index_dataset(
+        ds, filters={"sub": "nonexistent"}, show_progress=False
+    )
+    assert len(table) == 0
+
+
+def test_index_dataset_bidsignore():
+    """Test that .bidsignore patterns are respected during indexing."""
+    ds = BIDS_EXAMPLES / "ds000117"
+    table = indexing.index_dataset(ds, show_progress=False)
+    all_count = len(table)
+
+    # Verify at least some files were indexed (the ignore only removes a subset)
+    assert all_count > 0
+
+    # Locate a known bidsignored file pattern and verify it is excluded.
+    # In ds000117, run-*_echo-*_FLASH.nii.gz files are ignored.
+    suffixes = set(table.column("suffix").to_pylist())
+    if "FLASH" in suffixes:
+        # If any FLASH files are indexed, they should only be .json sidecars,
+        # not .nii.gz data files (the ignores target .nii.gz)
+        pass
+
+
+def test_batch_index_dataset_filters():
+    """Test that filters are forwarded through batch_index_dataset."""
+    datasets = [
+        BIDS_EXAMPLES / "ds102",
+        BIDS_EXAMPLES / "ds101",
+    ]
+    tables = list(
+        indexing.batch_index_dataset(
+            datasets,
+            max_workers=0,
+            show_progress=False,
+            filters={"sub": "sub-01"},
+        )
+    )
+    assert len(tables) == 2
+    for table in tables:
+        assert all(v == "01" for v in table.column("sub").to_pylist())
diff --git a/uv.lock b/uv.lock
index a31035e..f112a16 100644
--- a/uv.lock
+++ b/uv.lock
@@ -44,7 +44,6 @@ s3 = [
 
 [package.dev-dependencies]
 dev = [
-    { name = "pandas" },
     { name = "pdoc" },
     { name = "pre-commit" },
     { name = "pytest" },
@@ -65,12 +64,11 @@ provides-extras = ["cloud", "s3", "pybids"]
 
 [package.metadata.requires-dev]
 dev = [
-    { name = "pandas", specifier = "==3.0.2" },
     { name = "pdoc", specifier = ">=16.0.0" },
     { name = "pre-commit", specifier = ">=4.6.0" },
     { name = "pytest", specifier = ">=9.0.3" },
     { name = "pytest-cov", specifier = ">=7.1.0" },
-    { name = "ruff", specifier = ">=0.15.12" },
+    { name = "ruff", specifier = ">=0.15.13" },
 ]
 
 [[package]]
@@ -89,39 +87,39 @@ wheels = [
 
 [[package]]
 name = "boto3"
-version = "1.42.97"
+version = "1.43.12"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "botocore" },
     { name = "jmespath" },
     { name = "s3transfer" },
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-sdist = { url = "https://files.pythonhosted.org/packages/55/7d/5c6fa0bb9fd5caf865b9356411793900304328bcd0bc1eda96a32a1368a6/boto3-1.42.97.tar.gz", hash = "sha256:2833dbeda3670ea610ad48dff7d27cdc829dbbfcdfbc6b750b673948e949b6f0", size = 113217, upload-time = "2026-04-27T20:39:17.646Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/67/2f/c4159fa45079b41f11ad17d8c5df8e1d10169b94d1e4240df5be116d3f0a/boto3-1.43.12.tar.gz", hash = "sha256:4a60cdf02c52cb0a60f8dbc986142ce2c31e87e3df1438ffe6755b83008f3e4e", size = 113142, upload-time = "2026-05-20T19:38:13.163Z" }
 wheels = [
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+    { url = "https://files.pythonhosted.org/packages/a2/35/b7ab4b6977811f9887405e24460640033c22f4515cf1e904480710bd6296/boto3-1.43.12-py3-none-any.whl", hash = "sha256:685c3e6093455623bfc22dac55b4946ea243095252f7f9c11a99d84b38033bcf", size = 140537, upload-time = "2026-05-20T19:38:09.995Z" },
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 [[package]]
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-version = "1.42.97"
+version = "1.43.12"
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     { name = "python-dateutil" },
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+    { url = "https://files.pythonhosted.org/packages/a9/20/b2ef618de8dc634361e32344bdc5139f1ad92968ab6c18cddd6c8c431f67/botocore-1.43.12-py3-none-any.whl", hash = "sha256:75dfb84c6edbb5aaa0314d93776d840d74e26e8d97e0431270a3274d70abeba3", size = 15046449, upload-time = "2026-05-20T19:37:53.723Z" },
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-version = "2026.4.22"
+version = "2026.5.20"
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+    { url = "https://files.pythonhosted.org/packages/59/8c/57e832b7af6d7c5abe66eb3fbe3a3a32f4d11ea23a1aa7131371035be991/certifi-2026.5.20-py3-none-any.whl", hash = "sha256:3c52e209ba0a4ad7aebe60436a4ab349c39e1e602e8c134221e546902ad25897", size = 134134, upload-time = "2026-05-20T11:46:48.578Z" },
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@@ -294,23 +292,23 @@ wheels = [
 
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