diff --git a/pixi.lock b/pixi.lock
index a9c9302..b001027 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -6,6 +6,8 @@ environments:
     - url: https://conda.anaconda.org/bioconda/
     indexes:
     - https://pypi.org/simple
+    options:
+      pypi-prerelease-mode: if-necessary-or-explicit
     packages:
       linux-64:
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@@ -14,7 +16,7 @@ environments:
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.3-py312h5d8c7f2_0.conda
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@@ -23,15 +25,15 @@ environments:
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-      - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.12.1-pyhcf101f3_0.conda
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-      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyhcf101f3_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.4-hb03c661_0.conda
@@ -56,7 +58,7 @@ environments:
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-      - conda: https://conda.anaconda.org/conda-forge/noarch/bokeh-3.8.2-pyhd8ed1ab_0.conda
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@@ -73,14 +75,14 @@ environments:
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@@ -88,7 +90,7 @@ environments:
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-      - conda: https://conda.anaconda.org/conda-forge/noarch/configargparse-1.7.1-pyhe01879c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/configargparse-1.7.5-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/connection_pool-0.0.3-pyhd3deb0d_0.tar.bz2
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@@ -114,13 +116,13 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/ffmpeg-8.0.0-gpl_hc3e963e_905.conda
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-      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.25.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.25.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fmt-11.2.0-h07f6e7f_0.conda
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       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
@@ -129,9 +131,9 @@ environments:
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       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.61.1-py312h8a5da7c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.62.0-py312h8a5da7c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/formulaic-0.2.4-pyhd8ed1ab_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.2-ha770c72_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.3-ha770c72_0.conda
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@@ -144,21 +146,21 @@ environments:
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@@ -171,11 +173,11 @@ environments:
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+  - lightning-utilities >=0.15.3
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   - packaging >17.1
-  - python >=3.9
+  - python >=3.10
   - pytorch >=2.0.0
   - setuptools
   - typing_extensions
@@ -14620,8 +14543,8 @@ packages:
   license_family: APACHE
   purls:
   - pkg:pypi/torchmetrics?source=hash-mapping
-  size: 396413
-  timestamp: 1756932778045
+  size: 398600
+  timestamp: 1773827733172
 - conda: https://conda.anaconda.org/conda-forge/linux-64/torchvision-0.24.0-cpu_py312_h56cfa8b_0.conda
   sha256: a22214010fd1f3398ad7ea8311e0d76b0f7750590b502b0a73f57c14ca806595
   md5: feb0c7bde000f25617408266492d2d2a
@@ -14669,9 +14592,9 @@ packages:
   - pkg:pypi/torchvision-extra-decoders?source=hash-mapping
   size: 64620
   timestamp: 1748570842723
-- conda: https://conda.anaconda.org/conda-forge/linux-64/tornado-6.5.3-py312h4c3975b_0.conda
-  sha256: bed440cad040f0fe76266f9a527feecbaf00385b68a96532aa69614fe5153f8e
-  md5: e03a4bf52d2170d64c816b2a52972097
+- conda: https://conda.anaconda.org/conda-forge/linux-64/tornado-6.5.5-py312h4c3975b_0.conda
+  sha256: 4629b1c9139858fb08bb357df917ffc12e4d284c57ff389806bb3ae476ef4e0a
+  md5: 2b37798adbc54fd9e591d24679d2133a
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=14
@@ -14681,11 +14604,11 @@ packages:
   license_family: Apache
   purls:
   - pkg:pypi/tornado?source=compressed-mapping
-  size: 850918
-  timestamp: 1765458857375
-- conda: https://conda.anaconda.org/conda-forge/linux-64/tornado-6.5.3-py313h07c4f96_0.conda
-  sha256: 6006d4e5a6ff99be052c939e43adee844a38f2dc148f44a7c11aa0011fd3d811
-  md5: 82da2dcf1ea3e298f2557b50459809e0
+  size: 859665
+  timestamp: 1774358032165
+- conda: https://conda.anaconda.org/conda-forge/linux-64/tornado-6.5.5-py313h07c4f96_0.conda
+  sha256: 9e8497e1ecca77d03c6be2d3b5f901dfe0ab99686af4fb94ab418b7d449ac547
+  md5: 6c0b0ae017b5bfd9c8d718217efd8f14
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=14
@@ -14694,9 +14617,9 @@ packages:
   license: Apache-2.0
   license_family: Apache
   purls:
-  - pkg:pypi/tornado?source=hash-mapping
-  size: 878109
-  timestamp: 1765458900582
+  - pkg:pypi/tornado?source=compressed-mapping
+  size: 882996
+  timestamp: 1774358035145
 - conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda
   sha256: 9ef8e47cf00e4d6dcc114eb32a1504cc18206300572ef14d76634ba29dfe1eb6
   md5: e5ce43272193b38c2e9037446c1d9206
@@ -14706,7 +14629,7 @@ packages:
   - python
   license: MPL-2.0 and MIT
   purls:
-  - pkg:pypi/tqdm?source=compressed-mapping
+  - pkg:pypi/tqdm?source=hash-mapping
   size: 94132
   timestamp: 1770153424136
 - conda: https://conda.anaconda.org/conda-forge/noarch/traitlets-5.14.3-pyhd8ed1ab_1.conda
@@ -14772,19 +14695,6 @@ packages:
   - pkg:pypi/typer?source=hash-mapping
   size: 117860
   timestamp: 1771292312899
-- conda: https://conda.anaconda.org/conda-forge/noarch/typer-slim-0.24.0-pyhcf101f3_0.conda
-  sha256: 50db0bc6556667f2f26e9b08f9da9b5de0a02f075bd9ca8724e32df86a822788
-  md5: 143f46bdcb6b202bed14d33d27616c1e
-  depends:
-  - python >=3.10
-  - typer >=0.23.0
-  - python
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/typer-slim?source=hash-mapping
-  size: 13310
-  timestamp: 1771292312903
 - conda: https://conda.anaconda.org/conda-forge/noarch/typing-3.10.0.0-pyhd8ed1ab_2.conda
   sha256: 92b084dfd77571be23ef84ad695bbea169e844821484b6d47d99f04ea4de32e8
   md5: 28abeb80aea7eb4914f3a7543a47e248
@@ -15122,20 +15032,20 @@ packages:
   - pytest-mypy ; extra == 'testing'
   - pytest ; extra == 'testing'
   requires_python: '>=3.9'
-- conda: https://conda.anaconda.org/conda-forge/linux-64/wayland-1.24.0-hd6090a7_1.conda
-  sha256: 3aa04ae8e9521d9b56b562376d944c3e52b69f9d2a0667f77b8953464822e125
-  md5: 035da2e4f5770f036ff704fa17aace24
+- conda: https://conda.anaconda.org/conda-forge/linux-64/wayland-1.25.0-hd6090a7_0.conda
+  sha256: ea374d57a8fcda281a0a89af0ee49a2c2e99cc4ac97cf2e2db7064e74e764bdb
+  md5: 996583ea9c796e5b915f7d7580b51ea6
   depends:
   - __glibc >=2.17,<3.0.a0
-  - libexpat >=2.7.1,<3.0a0
+  - libexpat >=2.7.4,<3.0a0
   - libffi >=3.5.2,<3.6.0a0
   - libgcc >=14
   - libstdcxx >=14
   license: MIT
   license_family: MIT
   purls: []
-  size: 329779
-  timestamp: 1761174273487
+  size: 334139
+  timestamp: 1773959575393
 - conda: https://conda.anaconda.org/conda-forge/noarch/wayland-protocols-1.47-hd8ed1ab_0.conda
   sha256: 9ab2c12053ea8984228dd573114ffc6d63df42c501d59fda3bf3aeb1eaa1d23e
   md5: 7da1571f560d4ba3343f7f4c48a79c76
@@ -15152,7 +15062,7 @@ packages:
   license: MIT
   license_family: MIT
   purls:
-  - pkg:pypi/wcwidth?source=compressed-mapping
+  - pkg:pypi/wcwidth?source=hash-mapping
   size: 71550
   timestamp: 1770634638503
 - conda: https://conda.anaconda.org/conda-forge/noarch/webcolors-25.10.0-pyhd8ed1ab_0.conda
@@ -15188,9 +15098,9 @@ packages:
   - pkg:pypi/websocket-client?source=hash-mapping
   size: 61391
   timestamp: 1759928175142
-- conda: https://conda.anaconda.org/conda-forge/noarch/werkzeug-3.1.6-pyhcf101f3_0.conda
-  sha256: 06e3d5bec9d2730a23ecf023b7cba329c0772c51f2704714c17b3080b0385113
-  md5: 2d9bfc6055e55ff58b2c359323a753d2
+- conda: https://conda.anaconda.org/conda-forge/noarch/werkzeug-3.1.7-pyhcf101f3_0.conda
+  sha256: 09241e315a7c82eda22873770c0c919a01a1b1e5f14665fb191ab1d18be66eff
+  md5: 38cf6cde8cb2068fc896c7248e60f8ab
   depends:
   - markupsafe >=2.1.1
   - python >=3.10
@@ -15198,9 +15108,9 @@ packages:
   license: BSD-3-Clause
   license_family: BSD
   purls:
-  - pkg:pypi/werkzeug?source=compressed-mapping
-  size: 257130
-  timestamp: 1771530143814
+  - pkg:pypi/werkzeug?source=hash-mapping
+  size: 258058
+  timestamp: 1774357640759
 - conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda
   sha256: d6cf2f0ebd5e09120c28ecba450556ce553752652d91795442f0e70f837126ae
   md5: bdbd7385b4a67025ac2dba4ef8cb6a8f
@@ -15235,9 +15145,9 @@ packages:
   - pkg:pypi/wrapt?source=hash-mapping
   size: 64608
   timestamp: 1756851740646
-- conda: https://conda.anaconda.org/conda-forge/noarch/wslink-2.5.5-pyhd8ed1ab_0.conda
-  sha256: a30083522306002ab179327eb1fd4e5f2686335cca789cc97aaad914bee2feb1
-  md5: 755b2c36ab87bbb590a8637ebb29e488
+- conda: https://conda.anaconda.org/conda-forge/noarch/wslink-2.5.6-pyhd8ed1ab_0.conda
+  sha256: 0754558be231485ee835b0db11bace246ecd5465143a355029b039803ea716b0
+  md5: d34454e27bb9ec7025cefccfa92908ad
   depends:
   - aiohttp <4
   - msgpack-python >=1,<2
@@ -15245,9 +15155,9 @@ packages:
   license: BSD-3-Clause
   license_family: BSD
   purls:
-  - pkg:pypi/wslink?source=compressed-mapping
-  size: 36608
-  timestamp: 1772704099716
+  - pkg:pypi/wslink?source=hash-mapping
+  size: 36729
+  timestamp: 1773305846931
 - conda: https://conda.anaconda.org/conda-forge/linux-64/x264-1!164.3095-h166bdaf_2.tar.bz2
   sha256: 175315eb3d6ea1f64a6ce470be00fa2ee59980108f246d3072ab8b977cb048a5
   md5: 6c99772d483f566d59e25037fea2c4b1
@@ -15304,7 +15214,7 @@ packages:
   license: Apache-2.0
   license_family: APACHE
   purls:
-  - pkg:pypi/xarray?source=compressed-mapping
+  - pkg:pypi/xarray?source=hash-mapping
   size: 1011911
   timestamp: 1771083999178
 - conda: https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.1-h4f16b4b_2.conda
@@ -15699,7 +15609,7 @@ packages:
   license: Apache-2.0
   license_family: Apache
   purls:
-  - pkg:pypi/yarl?source=compressed-mapping
+  - pkg:pypi/yarl?source=hash-mapping
   size: 147028
   timestamp: 1772409590700
 - conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.9.4-pyhd8ed1ab_0.conda
@@ -15716,76 +15626,42 @@ packages:
   - pkg:pypi/yte?source=hash-mapping
   size: 16215
   timestamp: 1764250734338
-- conda: https://conda.anaconda.org/conda-forge/linux-64/z5py-2.0.20-py312h473be34_2.conda
-  sha256: 3d98fb402c95309754d9bfc1832ef01ecb38458106feb3d6cf463f7eddb77bcb
-  md5: f2126332dc83c9a1e3d70727a87b7d91
+- conda: https://conda.anaconda.org/conda-forge/linux-64/z5py-2.1.2-py312h64dc76f_1.conda
+  sha256: 51d27275f9a3089c153c0bb4e7038023755f4a6e58c4d3eae4d1899b56ccdb2c
+  md5: f0e96f3b0eba68ed00b264e4d3af09ce
   depends:
   - __glibc >=2.17,<3.0.a0
   - blosc >=1.21.6,<2.0a0
   - bzip2 >=1.0.8,<2.0a0
-  - libgcc >=13
-  - liblzma >=5.8.1,<6.0a0
-  - libstdcxx >=13
+  - libgcc >=14
+  - liblzma >=5.8.2,<6.0a0
+  - libstdcxx >=14
   - libzlib >=1.3.1,<2.0a0
-  - numpy >=1.19,<3
+  - lz4-c >=1.10.0,<1.11.0a0
+  - numpy >=1.23,<3
   - python >=3.12,<3.13.0a0
   - python_abi 3.12.* *_cp312
   license: MIT
   license_family: MIT
   purls: []
-  size: 731439
-  timestamp: 1746302625876
-- pypi: https://files.pythonhosted.org/packages/44/15/bb13b4913ef95ad5448490821eee4671d0e67673342e4d4070854e5fe081/zarr-3.1.5-py3-none-any.whl
+  size: 815224
+  timestamp: 1773911296984
+- pypi: https://files.pythonhosted.org/packages/de/7c/ba8ca8cbe9dbef8e83a95fc208fed8e6686c98b4719aaa0aa7f3d31fe390/zarr-3.1.6-py3-none-any.whl
   name: zarr
-  version: 3.1.5
-  sha256: 29cd905afb6235b94c09decda4258c888fcb79bb6c862ef7c0b8fe009b5c8563
+  version: 3.1.6
+  sha256: b5a82c5079d1c3d4ee8f06746fa3b9a98a7d804300fa3f4be154362a33e1207e
   requires_dist:
   - donfig>=0.8
   - google-crc32c>=1.5
   - numcodecs>=0.14
-  - numpy>=1.26
+  - numpy>=2.0
   - packaging>=22.0
-  - typing-extensions>=4.9
+  - typing-extensions>=4.12
   - typer ; extra == 'cli'
-  - astroid<4 ; extra == 'docs'
-  - griffe-inherited-docstrings ; extra == 'docs'
-  - markdown-exec[ansi] ; extra == 'docs'
-  - mike>=2.1.3 ; extra == 'docs'
-  - mkdocs-material[imaging]>=9.6.14 ; extra == 'docs'
-  - mkdocs-redirects>=1.2.0 ; extra == 'docs'
-  - mkdocs>=1.6.1 ; extra == 'docs'
-  - mkdocstrings-python>=1.16.10 ; extra == 'docs'
-  - mkdocstrings>=0.29.1 ; extra == 'docs'
-  - numcodecs[msgpack] ; extra == 'docs'
-  - pytest ; extra == 'docs'
-  - rich ; extra == 'docs'
-  - ruff ; extra == 'docs'
-  - s3fs>=2023.10.0 ; extra == 'docs'
-  - towncrier ; extra == 'docs'
   - cupy-cuda12x ; extra == 'gpu'
-  - rich ; extra == 'optional'
   - universal-pathlib ; extra == 'optional'
   - fsspec>=2023.10.0 ; extra == 'remote'
   - obstore>=0.5.1 ; extra == 'remote'
-  - botocore ; extra == 'remote-tests'
-  - fsspec>=2023.10.0 ; extra == 'remote-tests'
-  - moto[s3,server] ; extra == 'remote-tests'
-  - obstore>=0.5.1 ; extra == 'remote-tests'
-  - requests ; extra == 'remote-tests'
-  - s3fs>=2023.10.0 ; extra == 'remote-tests'
-  - coverage>=7.10 ; extra == 'test'
-  - hypothesis ; extra == 'test'
-  - mypy ; extra == 'test'
-  - numpydoc ; extra == 'test'
-  - packaging ; extra == 'test'
-  - pytest-accept ; extra == 'test'
-  - pytest-asyncio ; extra == 'test'
-  - pytest-cov ; extra == 'test'
-  - pytest-xdist ; extra == 'test'
-  - pytest<8.4 ; extra == 'test'
-  - rich ; extra == 'test'
-  - tomlkit ; extra == 'test'
-  - uv ; extra == 'test'
   requires_python: '>=3.11'
 - conda: https://conda.anaconda.org/conda-forge/noarch/zarr-3.1.5-pyhcf101f3_0.conda
   sha256: c36bec7d02d2f227409fcc4cf586cf3a658af068b58374de7f8f2d0b5c1c84f9
@@ -15915,18 +15791,17 @@ packages:
   - pkg:pypi/zipp?source=hash-mapping
   size: 24194
   timestamp: 1764460141901
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda
-  sha256: 5d7c0e5f0005f74112a34a7425179f4eb6e73c92f5d109e6af4ddeca407c92ab
-  md5: c9f075ab2f33b3bbee9e62d4ad0a6cd8
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.2-h25fd6f3_2.conda
+  sha256: 245c9ee8d688e23661b95e3c6dd7272ca936fabc03d423cdb3cdee1bbcf9f2f2
+  md5: c2a01a08fc991620a74b32420e97868a
   depends:
   - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - libzlib 1.3.1 hb9d3cd8_2
+  - libzlib 1.3.2 h25fd6f3_2
   license: Zlib
   license_family: Other
   purls: []
-  size: 92286
-  timestamp: 1727963153079
+  size: 95931
+  timestamp: 1774072620848
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.2.5-hde8ca8f_1.conda
   sha256: 84ea17cb646d8a916d9335415f57c9e5dd001de158972322c714ebe1b72670b0
   md5: c860578a89dc9b6003d600181612287c
diff --git a/pyproject.toml b/pyproject.toml
index 5d2e523..26e6a07 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,7 @@ platforms = ["linux-64"]
 
 [tool.pixi.feature.runtime.dependencies]
 snakemake = ">=9.5.1,<10"
-snakebids = ">=0.14.0,<0.15"
+snakebids = ">=0.15.0,<0.16"
 snakemake-storage-plugin-s3 = ">=0.3.3,<0.4"
 snakemake-storage-plugin-gcs = ">=1.1.4,<2"
 gcsfs = ">=2025.5.1,<2026"
diff --git a/spimquant/workflow/Snakefile b/spimquant/workflow/Snakefile
index 5c0394d..b83ae82 100644
--- a/spimquant/workflow/Snakefile
+++ b/spimquant/workflow/Snakefile
@@ -3,8 +3,15 @@ import os
 from zarrnii import ZarrNii
 from snakemake.utils import format
 from snakebids import bids, generate_inputs, get_wildcard_constraints, set_bids_spec
+import snakebids
 
-set_bids_spec("v0_11_0")
+# update v15 spec to add template entity
+spec = snakebids.paths.specs.v0_15_0()
+tpl_spec = spec[0].copy()
+tpl_spec["entity"] = "template"
+tpl_spec["tag"] = "tpl"
+spec.insert(0, tpl_spec)
+snakebids.set_bids_spec(spec)
 
 
 configfile: "config/snakebids.yml"
@@ -200,7 +207,7 @@ rule all_fieldfrac_tune:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 stain="{stain}",
                 level="{level}",
                 desc="otsu+k{k}i{i}",
@@ -233,9 +240,10 @@ rule all_register:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="xfm",
                 stain="{stain}",
-                space="{template}",
+                from_="SPIM",
+                to="{template}",
                 suffix="regqc.html",
                 **inputs["spim"].wildcards,
             ),
@@ -249,7 +257,7 @@ rule all_vessels:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="vessels",
                 stain="{stain}",
                 level="{level}",
                 desc="{desc}",
@@ -269,7 +277,7 @@ rule all_segment:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="featuremap",
                 seg="{seg}",
                 space="{template}",
                 desc="{desc}",
@@ -299,7 +307,7 @@ rule all_segment:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 stain="{stain}",
                 level="{level}",
                 desc="{desc}",
@@ -315,25 +323,7 @@ rule all_segment:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
-                stain="{stain}",
-                seg="{seg}",
-                desc="deform",
-                level="{level}",
-                from_="{template}",
-                suffix="dseg.{ext}",
-                **inputs["spim"].wildcards,
-            ),
-            stain=stains_for_seg,
-            level=config["registration_level"],
-            seg=atlas_segs,
-            template=config["template"],
-            ext=["tsv", "itksnap.txt"],
-        ),
-        inputs["spim"].expand(
-            bids(
-                root=root,
-                datatype="micr",
+                datatype="seg",
                 stain="{stain}",
                 level="{level}",
                 desc="{desc}",
@@ -347,7 +337,7 @@ rule all_segment:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 stain="{stain}",
                 space="{template}",
                 desc="{desc}",
@@ -358,6 +348,17 @@ rule all_segment:
             template=config["template"],
             desc=config["seg_method"],
         ),
+        expand(
+            bids(
+                root=root,
+                template="{template}",
+                seg="{seg}",
+                suffix="dseg.{ext}",
+            ),
+            seg=atlas_segs,
+            template=config["template"],
+            ext=["tsv", "itksnap.txt"],
+        ),
 
 
 rule all_segment_coloc:
@@ -365,7 +366,7 @@ rule all_segment_coloc:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="featuremap",
                 seg="{seg}",
                 space="{template}",
                 desc="{desc}",
@@ -380,7 +381,7 @@ rule all_segment_coloc:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 desc="{desc}",
                 space="{template}",
                 suffix="coloccounts.nii.gz",
@@ -408,8 +409,9 @@ rule all_mri_reg:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="anat",
-                space="SPIM",
+                datatype="xfm",
+                from_=f"{mri_suffix}",
+                to="SPIM",
                 suffix="regqc.html",
                 **inputs["spim"].wildcards,
             ),
@@ -421,7 +423,7 @@ rule all_spim_patches:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 stain="{stain}",
                 seg="{seg}",
                 from_="{template}",
@@ -439,7 +441,7 @@ rule all_spim_patches:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 stain="{stain}",
                 seg="{seg}",
                 from_="{template}",
@@ -461,7 +463,7 @@ rule all_imaris_crops:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 seg="{seg}",
                 from_="{template}",
                 level="{level}",
diff --git a/spimquant/workflow/rules/common.smk b/spimquant/workflow/rules/common.smk
index d1ad864..fc33c75 100644
--- a/spimquant/workflow/rules/common.smk
+++ b/spimquant/workflow/rules/common.smk
@@ -3,7 +3,6 @@ Common utility functions for SPIMquant workflows.
 
 This module provides shared helper functions used across multiple workflow rules:
 
-- bids_tpl(): BIDS path constructor for template-specific files
 - resources_path(): Path resolver for resources directory
 - get_template_path(): Template file locator with optional cropping
 - get_template_for_reg(): Registration-specific template selector
@@ -14,12 +13,6 @@ organization following BIDS conventions.
 """
 
 from pathlib import Path
-from snakebids import bids
-
-
-def bids_tpl(root, template, **entities):
-    """bids() wrapper for files in tpl-template folder"""
-    return str(Path(bids(root=root, tpl=template)) / bids(tpl=template, **entities))
 
 
 def resources_path(path):
@@ -38,14 +31,14 @@ def get_template_path(root, template, template_crop=None):
         suffix = "anat"
 
     if template_crop is not None:
-        return bids_tpl(
+        return bids(
             root=root,
             template=template,
             desc=f"{template_crop}crop",
             suffix=f"{suffix}.nii.gz",
         )
     else:
-        return bids_tpl(root=root, template=template, suffix=f"{suffix}.nii.gz")
+        return bids(root=root, template=template, suffix=f"{suffix}.nii.gz")
 
 
 def get_template_for_reg(wildcards):
@@ -58,9 +51,7 @@ def get_template_for_reg(wildcards):
     if config.get("template_crop") is not None:
         return get_template_path(root, wildcards.template, config["template_crop"])
     else:
-        return bids_tpl(
-            root=root, template=wildcards.template, suffix=f"{suffix}.nii.gz"
-        )
+        return bids(root=root, template=wildcards.template, suffix=f"{suffix}.nii.gz")
 
 
 def get_stains_all_subjects():
@@ -79,7 +70,7 @@ def get_regionprops_parquet(wildcards):
     if do_vessels:
         return bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             desc="{desc}+vessels",
             space="{template}",
             vessels=stain_for_vessels,
@@ -89,7 +80,7 @@ def get_regionprops_parquet(wildcards):
     else:
         return bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             desc="{desc}",
             space="{template}",
             suffix="regionprops.parquet",
diff --git a/spimquant/workflow/rules/counts.smk b/spimquant/workflow/rules/counts.smk
index dc99596..8e8f0b1 100644
--- a/spimquant/workflow/rules/counts.smk
+++ b/spimquant/workflow/rules/counts.smk
@@ -4,7 +4,7 @@ rule counts_per_voxel:
         ref_spim=inputs["spim"].path,
         regionprops_parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             stain="{stain}",
             desc="{desc}",
             suffix="regionprops.parquet",
@@ -16,7 +16,7 @@ rule counts_per_voxel:
     output:
         counts_nii=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             level="{level}",
             stain="{stain}",
             desc="{desc}",
@@ -35,10 +35,10 @@ rule counts_per_voxel_template:
     """Calculate counts per voxel based on points
     in template space"""
     input:
-        template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+        template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
         regionprops_parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             space="{template}",
             desc="{desc}",
             suffix="regionprops.parquet",
@@ -49,7 +49,7 @@ rule counts_per_voxel_template:
     output:
         counts_nii=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             space="{template}",
             desc="{desc}",
@@ -68,10 +68,10 @@ rule coloc_per_voxel_template:
     """Calculate coloc counts per voxel based on points
     in template space"""
     input:
-        template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+        template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
         coloc_parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             space="{template}",
             desc="{desc}",
             suffix="coloc.parquet",
@@ -82,7 +82,7 @@ rule coloc_per_voxel_template:
     output:
         counts_nii=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             space="{template}",
             desc="{desc}",
             suffix="coloccounts.nii.gz",
diff --git a/spimquant/workflow/rules/fieldfrac.smk b/spimquant/workflow/rules/fieldfrac.smk
index d0759a3..d29e95b 100644
--- a/spimquant/workflow/rules/fieldfrac.smk
+++ b/spimquant/workflow/rules/fieldfrac.smk
@@ -10,7 +10,7 @@ rule fieldfrac:
     input:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="{datatype}",
             stain="{stain}",
             level=config["segmentation_level"],
             desc="{desc}",
@@ -23,7 +23,7 @@ rule fieldfrac:
     output:
         fieldfrac_nii=bids(
             root=root,
-            datatype="micr",
+            datatype="{datatype,seg|vessels}",
             stain="{stain}",
             level="{level}",
             desc="{desc}",
@@ -42,7 +42,7 @@ rule map_fieldfrac_img_to_seg_tsv:
     input:
         img=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="{desc}",
@@ -51,22 +51,19 @@ rule map_fieldfrac_img_to_seg_tsv:
         ),
         dseg=bids(
             root=root,
-            datatype="micr",
+            datatype="parc",
             seg="{seg}",
-            desc="deform",
             level="{level}",
             from_="{template}",
             suffix="dseg.nii.gz",
             **inputs["spim"].wildcards,
         ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     output:
         tsv=temp(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg="{seg}",
                 from_="{template}",
                 stain="{stain}",
diff --git a/spimquant/workflow/rules/groupstats.smk b/spimquant/workflow/rules/groupstats.smk
index 1fec69e..3e41c6f 100644
--- a/spimquant/workflow/rules/groupstats.smk
+++ b/spimquant/workflow/rules/groupstats.smk
@@ -17,7 +17,7 @@ rule perform_group_stats:
         segstats_tsvs=lambda wildcards: inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg=wildcards.seg,
                 from_=wildcards.template,
                 desc=wildcards.desc,
@@ -67,9 +67,7 @@ rule create_stats_heatmap:
             desc="{desc}",
             suffix="groupstats.tsv",
         ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         metric_columns=expand(
             "{stain}+{metric}", stain=stains_for_seg, metric=config["seg_metrics"]
@@ -109,12 +107,8 @@ rule map_groupstats_to_template_nii:
             desc="{desc}",
             suffix="groupstats.tsv",
         ),
-        dseg=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"
-        ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        dseg=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         label_column="index",
         feature_column="{metric}_{stat}",
@@ -148,7 +142,7 @@ rule concat_subj_parquet:
         parquet_files=inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 space="{template}",
                 desc="{desc}",
                 suffix="{suffix}.parquet",
@@ -177,7 +171,7 @@ rule group_counts_per_voxel:
     """Calculate counts per voxel based on concatenated points
     in template space"""
     input:
-        template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+        template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
         regionprops_parquet=bids(
             root=root,
             datatype="group",
@@ -208,7 +202,7 @@ rule group_coloc_counts_per_voxel:
     """Calculate counts per voxel based on concatenated coloc points
     in template space"""
     input:
-        template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+        template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
         coloc_parquet=bids(
             root=root,
             datatype="group",
@@ -248,7 +242,7 @@ rule concat_subj_parquet_contrast:
         parquet_files=inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 space="{template}",
                 desc="{desc}",
                 suffix="{suffix}.parquet",
@@ -281,7 +275,7 @@ rule group_counts_per_voxel_contrast:
     """Calculate counts per voxel based on concatenated points
     in template space, filtered by contrast"""
     input:
-        template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+        template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
         regionprops_parquet=bids(
             root=root,
             datatype="group",
@@ -314,7 +308,7 @@ rule group_coloc_counts_per_voxel_contrast:
     """Calculate counts per voxel based on concatenated coloc points
     in template space, filtered by contrast"""
     input:
-        template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+        template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
         coloc_parquet=bids(
             root=root,
             datatype="group",
@@ -357,7 +351,7 @@ rule concat_subj_segstats_contrast:
         segstats_tsvs=lambda wildcards: inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg=wildcards.seg,
                 from_=wildcards.template,
                 desc=wildcards.desc,
@@ -410,12 +404,8 @@ rule map_groupavg_segstats_to_template_nii:
             contrast="{contrast_column}+{contrast_value}",
             suffix="groupavgsegstats.tsv",
         ),
-        dseg=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"
-        ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        dseg=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         label_column="index",
         feature_column="{metric}",
diff --git a/spimquant/workflow/rules/heatmaps.smk b/spimquant/workflow/rules/heatmaps.smk
index 2ef9cc1..6fcf81c 100644
--- a/spimquant/workflow/rules/heatmaps.smk
+++ b/spimquant/workflow/rules/heatmaps.smk
@@ -4,26 +4,22 @@ rule map_segstats_tsv_dseg_to_template_nii:
     input:
         tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             desc="{desc}",
             suffix="mergedsegstats.tsv",
             **inputs["spim"].wildcards,
         ),
-        dseg=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"
-        ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        dseg=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         label_column="index",
         feature_column="{suffix}",
     output:
         nii=bids(
             root=root,
-            datatype="micr",
+            datatype="featuremap",
             seg="{seg}",
             space="{template}",
             desc="{desc}",
@@ -43,7 +39,7 @@ rule map_segstats_tsv_dseg_to_subject_nii:
     input:
         tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             desc="{desc}",
@@ -52,24 +48,21 @@ rule map_segstats_tsv_dseg_to_subject_nii:
         ),
         dseg=bids(
             root=root,
-            datatype="micr",
+            datatype="parc",
             seg="{seg}",
-            desc="deform",
             level="{level}",
             from_="{template}",
             suffix="dseg.nii.gz",
             **inputs["spim"].wildcards,
         ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         label_column="index",
         feature_column="{suffix}",
     output:
         nii=bids(
             root=root,
-            datatype="micr",
+            datatype="featuremap",
             seg="{seg}",
             level="{level}",
             from_="{template}",
@@ -89,7 +82,7 @@ rule deform_fieldfrac_nii_to_template_nii:
     input:
         flo=bids(
             root=root,
-            datatype="micr",
+            datatype="{datatype}",
             stain="{stain}",
             level="{level}",
             desc="{desc}",
@@ -101,7 +94,7 @@ rule deform_fieldfrac_nii_to_template_nii:
     output:
         nii=bids(
             root=root,
-            datatype="micr",
+            datatype="{datatype,seg|vessels}",
             stain="{stain}",
             level="{level}",
             desc="{desc}",
diff --git a/spimquant/workflow/rules/import.smk b/spimquant/workflow/rules/import.smk
index e21df24..36f7f5e 100644
--- a/spimquant/workflow/rules/import.smk
+++ b/spimquant/workflow/rules/import.smk
@@ -72,13 +72,13 @@ rule import_template_anat:
             ancient(resources_path(config["templates"][wildcards.template]["anat"]))
         ),
     output:
-        anat=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+        anat=bids(root=root, template="{template}", suffix="anat.nii.gz"),
     threads: 1
     resources:
         mem_mb=1500,
         runtime=15,
     log:
-        bids_tpl(
+        bids(
             root="logs",
             datatype="import_anat",
             template="{template}",
@@ -102,15 +102,13 @@ rule import_template_spim:
             )
         ),
     output:
-        anat=bids_tpl(
-            root=root, template="{template}", suffix=f"{stain_for_reg}.nii.gz"
-        ),
+        anat=bids(root=root, template="{template}", suffix=f"{stain_for_reg}.nii.gz"),
     threads: 1
     resources:
         mem_mb=1500,
         runtime=15,
     log:
-        bids_tpl(
+        bids(
             root="logs",
             datatype=f"import_template_spim_{stain_for_reg}",
             template="{template}",
@@ -126,15 +124,13 @@ rule import_mask:
             ancient(resources_path(config["templates"][wildcards.template]["mask"]))
         ),
     output:
-        mask=bids_tpl(
-            root=root, template="{template}", desc="brain", suffix="mask.nii.gz"
-        ),
+        mask=bids(root=root, template="{template}", desc="brain", suffix="mask.nii.gz"),
     threads: 1
     resources:
         mem_mb=1500,
         runtime=15,
     log:
-        bids_tpl(
+        bids(
             root="logs",
             datatype="import_mask",
             template="{template}",
@@ -175,9 +171,7 @@ rule import_dseg:
             )
         ),
     output:
-        dseg=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"
-        ),
+        dseg=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"),
     threads: 1
     resources:
         mem_mb=1500,
@@ -198,7 +192,7 @@ rule import_lut_tsv:
             )
         ),
     output:
-        tsv=bids_tpl(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
+        tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     threads: 1
     resources:
         mem_mb=1500,
@@ -211,7 +205,7 @@ rule import_DSURQE_tsv:
     input:
         csv=storage(config["templates"]["DSURQE"]["atlases"]["all"]["custom_csv"]),
     output:
-        tsv=bids_tpl(root=root, template="DSURQE", seg="all", suffix="dseg.tsv"),
+        tsv=bids(root=root, template="DSURQE", seg="all", suffix="dseg.tsv"),
     threads: 1
     resources:
         mem_mb=1500,
diff --git a/spimquant/workflow/rules/masking.smk b/spimquant/workflow/rules/masking.smk
index cc60b35..bc816e7 100644
--- a/spimquant/workflow/rules/masking.smk
+++ b/spimquant/workflow/rules/masking.smk
@@ -186,7 +186,7 @@ rule init_affine_reg:
         xfm_ras=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_="subject",
                 to="{template}",
                 type_="ras",
@@ -198,7 +198,7 @@ rule init_affine_reg:
         warped=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 space="{template}",
                 desc="initaffinewarped",
                 suffix="SPIM.nii.gz",
diff --git a/spimquant/workflow/rules/patches.smk b/spimquant/workflow/rules/patches.smk
index cb27392..b277662b 100644
--- a/spimquant/workflow/rules/patches.smk
+++ b/spimquant/workflow/rules/patches.smk
@@ -34,17 +34,14 @@ rule create_spim_patches:
         spim=inputs["spim"].path,
         dseg=bids(
             root=root,
-            datatype="micr",
+            datatype="parc",
             seg="{seg}",
-            desc="deform",
             level=config["registration_level"],
             from_="{template}",
             suffix="dseg.nii.gz",
             **inputs["spim"].wildcards,
         ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         patch_size=config.get("patch_size", [256, 256, 256]),
         n_patches=config.get("n_patches_per_label", 10),
@@ -84,7 +81,7 @@ rule create_mask_patches:
     input:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level=config["segmentation_level"],
             desc="{desc}",
@@ -93,17 +90,14 @@ rule create_mask_patches:
         ),
         dseg=bids(
             root=root,
-            datatype="micr",
+            datatype="parc",
             seg="{seg}",
-            desc="deform",
             level=config["registration_level"],
             from_="{template}",
             suffix="dseg.nii.gz",
             **inputs["spim"].wildcards,
         ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         patch_size=config.get("patch_size", [256, 256, 256]),
         n_patches=config.get("n_patches_per_label", 10),
@@ -115,7 +109,7 @@ rule create_mask_patches:
         patches_dir=directory(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 stain="{stain}",
                 seg="{seg}",
                 from_="{template}",
@@ -143,7 +137,7 @@ rule create_corrected_spim_patches:
     input:
         corrected=bids(
             root=work,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level=config["segmentation_level"],
             desc="corrected{corrmethod}",
@@ -152,17 +146,14 @@ rule create_corrected_spim_patches:
         ),
         dseg=bids(
             root=root,
-            datatype="micr",
+            datatype="parc",
             seg="{seg}",
-            desc="deform",
             level=config["registration_level"],
             from_="{template}",
             suffix="dseg.nii.gz",
             **inputs["spim"].wildcards,
         ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         patch_size=config.get("patch_size", [256, 256, 256]),
         n_patches=config.get("n_patches_per_label", 10),
@@ -174,7 +165,7 @@ rule create_corrected_spim_patches:
         patches_dir=directory(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 stain="{stain}",
                 seg="{seg}",
                 from_="{template}",
@@ -203,17 +194,14 @@ rule create_imaris_crops:
         spim=inputs["spim"].path,
         dseg=bids(
             root=root,
-            datatype="micr",
+            datatype="parc",
             seg="{seg}",
-            desc="deform",
             level=config["registration_level"],
             from_="{template}",
             suffix="dseg.nii.gz",
             **inputs["spim"].wildcards,
         ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         crop_labels=config.get("crop_labels", None),
         hires_level=0,  # input is the raw data
@@ -222,7 +210,7 @@ rule create_imaris_crops:
         crops_dir=directory(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="seg",
                 seg="{seg}",
                 from_="{template}",
                 level="{level}",
diff --git a/spimquant/workflow/rules/preproc_mri.smk b/spimquant/workflow/rules/preproc_mri.smk
index 8fc80cd..d18af10 100644
--- a/spimquant/workflow/rules/preproc_mri.smk
+++ b/spimquant/workflow/rules/preproc_mri.smk
@@ -120,7 +120,7 @@ rule register_mri_to_first:
         xfm_ras=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_=f"{mri_suffix}",
                 to=f"{mri_suffix}ref",
                 type_="ras",
@@ -152,7 +152,7 @@ rule resample_mri_to_first:
         moving=get_mri_by_index,
         xfm_ras=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_=f"{mri_suffix}",
             to=f"{mri_suffix}ref",
             type_="ras",
@@ -230,7 +230,7 @@ rule rigid_nlin_reg_mri_to_template:
     brain-masking if a suitable model is found/trained.
     """
     input:
-        template=bids_tpl(root=root, template="{template}", suffix="anat.nii.gz"),
+        template=bids(root=root, template="{template}", suffix="anat.nii.gz"),
         subject=bids(
             root=root,
             datatype="anat",
@@ -247,7 +247,7 @@ rule rigid_nlin_reg_mri_to_template:
         xfm_ras=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_=f"{mri_suffix}",
                 to="{template}",
                 type_="ras",
@@ -263,7 +263,7 @@ rule rigid_nlin_reg_mri_to_template:
         warp=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_=f"{mri_suffix}",
                 to="{template}",
                 suffix="warp.nii.gz",
@@ -277,7 +277,7 @@ rule rigid_nlin_reg_mri_to_template:
         invwarp=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_="{template}",
                 to=f"{mri_suffix}",
                 suffix="warp.nii.gz",
@@ -291,7 +291,7 @@ rule rigid_nlin_reg_mri_to_template:
         warped=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 space="{template}",
                 desc="deformwarped",
                 suffix=f"{mri_suffix}.nii.gz",
@@ -343,7 +343,7 @@ rule all_tune_mri_mask:
 
 rule transform_template_mask_to_mri:
     input:
-        mask=bids_tpl(
+        mask=bids(
             root=root,
             template=config["template_mri"],
             desc="brain",
@@ -358,7 +358,7 @@ rule transform_template_mask_to_mri:
         ),
         xfm_ras=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_=f"{mri_suffix}",
             to=config["template_mri"],
             type_="ras",
@@ -372,7 +372,7 @@ rule transform_template_mask_to_mri:
         ),
         invwarp=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_=config["template_mri"],
             to=f"{mri_suffix}",
             suffix="warp.nii.gz",
@@ -483,7 +483,7 @@ rule affine_nlin_reg_mri_to_spim:
         xfm_ras=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_=f"{mri_suffix}",
                 to="SPIM",
                 type_="ras",
@@ -500,7 +500,7 @@ rule affine_nlin_reg_mri_to_spim:
         warp=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_=f"{mri_suffix}",
                 to="SPIM",
                 suffix="warp.nii.gz",
@@ -515,7 +515,7 @@ rule affine_nlin_reg_mri_to_spim:
         invwarp=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_="SPIM",
                 to=f"{mri_suffix}",
                 suffix="warp.nii.gz",
@@ -530,7 +530,7 @@ rule affine_nlin_reg_mri_to_spim:
         linwarped=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 space="SPIM",
                 desc="linearwarped",
                 suffix=f"{mri_suffix}.nii.gz",
@@ -545,7 +545,7 @@ rule affine_nlin_reg_mri_to_spim:
         warped=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 space="SPIM",
                 desc="deformwarped",
                 suffix=f"{mri_suffix}.nii.gz",
@@ -605,7 +605,7 @@ rule compose_mri_to_spim_warp:
         ),
         xfm_ras=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_=f"{mri_suffix}",
             to="SPIM",
             type_="ras",
@@ -620,7 +620,7 @@ rule compose_mri_to_spim_warp:
         ),
         warp=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_=f"{mri_suffix}",
             to="SPIM",
             suffix="warp.nii.gz",
@@ -633,7 +633,7 @@ rule compose_mri_to_spim_warp:
         ),
         invwarp=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_="SPIM",
             to=f"{mri_suffix}",
             suffix="warp.nii.gz",
@@ -647,7 +647,7 @@ rule compose_mri_to_spim_warp:
     output:
         xfm_composite=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_=f"{mri_suffix}",
             to="SPIM",
             suffix="xfm.nii.gz",
@@ -655,7 +655,7 @@ rule compose_mri_to_spim_warp:
         ),
         xfm_composite_inv=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_="SPIM",
             to=f"{mri_suffix}",
             suffix="xfm.nii.gz",
@@ -679,7 +679,7 @@ rule all_tune_mri_spim_reg:
         inputs["spim"].expand(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 space="SPIM",
                 desc="deformwarped",
                 suffix=f"{mri_suffix}.nii.gz",
@@ -812,7 +812,7 @@ rule mri_spim_registration_qc_report:
         ),
         warped_affine=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             space="SPIM",
             desc="linearwarped",
             suffix=f"{mri_suffix}.nii.gz",
@@ -825,7 +825,7 @@ rule mri_spim_registration_qc_report:
         ),
         warped_deform=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             space="SPIM",
             desc="deformwarped",
             suffix=f"{mri_suffix}.nii.gz",
@@ -842,8 +842,9 @@ rule mri_spim_registration_qc_report:
     output:
         report_html=bids(
             root=root,
-            datatype="anat",
-            space="SPIM",
+            datatype="xfm",
+            from_=f"{mri_suffix}",
+            to="SPIM",
             suffix="regqc.html",
             **inputs["spim"].wildcards,
         ),
diff --git a/spimquant/workflow/rules/regionprops.smk b/spimquant/workflow/rules/regionprops.smk
index 5651f50..f40036e 100644
--- a/spimquant/workflow/rules/regionprops.smk
+++ b/spimquant/workflow/rules/regionprops.smk
@@ -3,7 +3,7 @@ rule compute_filtered_regionprops:
     input:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level=config["segmentation_level"],
             desc="{desc}",
@@ -20,7 +20,7 @@ rule compute_filtered_regionprops:
         regionprops_parquet=temp(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 stain="{stain}",
                 desc="{desc}",
                 suffix="regionprops.parquet",
@@ -40,7 +40,7 @@ rule transform_regionprops_to_template:
     input:
         regionprops_parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             stain="{stain}",
             desc="{desc}",
             suffix="regionprops.parquet",
@@ -53,7 +53,7 @@ rule transform_regionprops_to_template:
         regionprops_transformed_parquet=temp(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 stain="{stain}",
                 desc="{desc}",
                 space="{template}",
@@ -75,7 +75,7 @@ rule aggregate_regionprops_across_stains:
         regionprops_parquets=expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 stain="{stain}",
                 desc="{desc}",
                 space="{template}",
@@ -90,7 +90,7 @@ rule aggregate_regionprops_across_stains:
     output:
         regionprops_aggregated_parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             desc="{desc}",
             space="{template}",
             suffix="regionprops.parquet",
@@ -114,7 +114,7 @@ rule colocalize_regionprops:
     input:
         regionprops_parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             desc="{desc}",
             space="{template}",
             suffix="regionprops.parquet",
@@ -128,7 +128,7 @@ rule colocalize_regionprops:
     output:
         coloc_parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             desc="{desc}",
             space="{template}",
             suffix="coloc.parquet",
@@ -151,7 +151,7 @@ rule sample_at_vessel_sdt:
     input:
         parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             desc="{desc}",
             space="{template}",
             suffix="regionprops.parquet",
@@ -159,7 +159,7 @@ rule sample_at_vessel_sdt:
         ),
         scalar=bids(
             root=root,
-            datatype="micr",
+            datatype="vessels",
             stain="{stain}",
             level=config["segmentation_level"],
             desc=config["vessel_seg_method"],
@@ -173,7 +173,7 @@ rule sample_at_vessel_sdt:
     output:
         parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             desc="{desc}+vessels",
             space="{template}",
             vessels="{stain}",
diff --git a/spimquant/workflow/rules/segmentation.smk b/spimquant/workflow/rules/segmentation.smk
index d69f008..bc95e73 100644
--- a/spimquant/workflow/rules/segmentation.smk
+++ b/spimquant/workflow/rules/segmentation.smk
@@ -35,7 +35,7 @@ rule gaussian_biasfield:
             directory(
                 bids(
                     root=work,
-                    datatype="micr",
+                    datatype="seg",
                     stain="{stain}",
                     level="{level}",
                     desc="correctedgaussian",
@@ -49,7 +49,7 @@ rule gaussian_biasfield:
             directory(
                 bids(
                     root=work,
-                    datatype="micr",
+                    datatype="seg",
                     stain="{stain}",
                     level="{level}",
                     desc="gaussian",
@@ -82,7 +82,7 @@ rule n4_biasfield:
             directory(
                 bids(
                     root=work,
-                    datatype="micr",
+                    datatype="seg",
                     stain="{stain}",
                     level="{level}",
                     desc="correctedn4",
@@ -111,7 +111,7 @@ rule multiotsu:
     input:
         corrected=bids(
             root=work,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="corrected{method}".format(method=config["correction_method"]),
@@ -127,7 +127,7 @@ rule multiotsu:
     output:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="otsu+k{k,[0-9]+}i{i,[0-9]+}",
@@ -136,7 +136,7 @@ rule multiotsu:
         ),
         thresholds_png=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="otsu+k{k,[0-9]+}i{i,[0-9]+}",
@@ -161,7 +161,7 @@ rule threshold:
     input:
         corrected=bids(
             root=work,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="corrected{method}".format(method=config["correction_method"]),
@@ -174,7 +174,7 @@ rule threshold:
     output:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="th{threshold,[0-9]+}",
@@ -199,7 +199,7 @@ rule clean_segmentation:
     input:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="{desc}",
@@ -213,7 +213,7 @@ rule clean_segmentation:
     output:
         exclude_mask=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="{desc}+cleaned",
@@ -222,7 +222,7 @@ rule clean_segmentation:
         ),
         cleaned_mask=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             stain="{stain}",
             level="{level}",
             desc="{desc}+cleaned",
@@ -253,7 +253,7 @@ rule deform_negative_mask_to_subject_nii:
     output:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="seg",
             desc="negative",
             level="{level}",
             from_="{template}",
diff --git a/spimquant/workflow/rules/segstats.smk b/spimquant/workflow/rules/segstats.smk
index 5effaed..816a307 100644
--- a/spimquant/workflow/rules/segstats.smk
+++ b/spimquant/workflow/rules/segstats.smk
@@ -4,23 +4,20 @@ rule map_regionprops_to_atlas_rois:
         regionprops_parquet=get_regionprops_parquet,
         dseg=bids(
             root=root,
-            datatype="micr",
+            datatype="parc",
             seg="{seg}",
-            desc="deform",
             level="{level}",
             from_="{template}",
             suffix="dseg.nii.gz",
             **inputs["spim"].wildcards,
         ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         coord_column_names=config["coord_column_names"],
     output:
         regionprops_tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             stain="{stain}",
@@ -32,7 +29,7 @@ rule map_regionprops_to_atlas_rois:
         counts_tsv=temp(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg="{seg}",
                 from_="{template}",
                 stain="{stain}",
@@ -54,25 +51,21 @@ rule map_coloc_to_atlas_rois:
     input:
         coloc_parquet=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             space="{template}",
             desc="{desc}",
             suffix="coloc.parquet",
             **inputs["spim"].wildcards,
         ),
-        dseg=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"
-        ),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"
-        ),
+        dseg=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"),
+        label_tsv=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
     params:
         coord_column_names=["template_coloc_x", "template_coloc_y", "template_coloc_z"],
     output:
         coloc_tsv=temp(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg="{seg}",
                 from_="{template}",
                 desc="{desc}",
@@ -83,7 +76,7 @@ rule map_coloc_to_atlas_rois:
         counts_tsv=temp(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg="{seg}",
                 from_="{template}",
                 desc="{desc}",
@@ -103,7 +96,7 @@ rule merge_into_segstats_tsv:
     input:
         regionprops_tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             stain="{stain}",
@@ -114,7 +107,7 @@ rule merge_into_segstats_tsv:
         ),
         counts_tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             stain="{stain}",
@@ -125,7 +118,7 @@ rule merge_into_segstats_tsv:
         ),
         fieldfrac_tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             stain="{stain}",
@@ -138,7 +131,7 @@ rule merge_into_segstats_tsv:
         tsv=temp(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg="{seg}",
                 from_="{template}",
                 stain="{stain}",
@@ -161,7 +154,7 @@ rule merge_into_colocsegstats_tsv:
     input:
         coloc_tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             desc="{desc}",
@@ -170,7 +163,7 @@ rule merge_into_colocsegstats_tsv:
         ),
         counts_tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             desc="{desc}",
@@ -179,7 +172,7 @@ rule merge_into_colocsegstats_tsv:
         ),
         fieldfrac_tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             stain=stains_for_seg[0],
@@ -194,7 +187,7 @@ rule merge_into_colocsegstats_tsv:
         tsv=temp(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg="{seg}",
                 from_="{template}",
                 desc="{desc}",
@@ -218,7 +211,7 @@ def get_coloc_tsv_input_kwargs():
         return {
             "coloc_tsv": bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg="{seg}",
                 from_="{template}",
                 desc="{desc}",
@@ -234,7 +227,7 @@ rule merge_indiv_and_coloc_segstats_tsv:
         indiv_tsvs=expand(
             bids(
                 root=root,
-                datatype="micr",
+                datatype="tabular",
                 seg="{seg}",
                 from_="{template}",
                 stain="{stain}",
@@ -251,7 +244,7 @@ rule merge_indiv_and_coloc_segstats_tsv:
     output:
         merged_tsv=bids(
             root=root,
-            datatype="micr",
+            datatype="tabular",
             seg="{seg}",
             from_="{template}",
             desc="{desc}",
diff --git a/spimquant/workflow/rules/templatereg.smk b/spimquant/workflow/rules/templatereg.smk
index c5d4973..cc449bd 100644
--- a/spimquant/workflow/rules/templatereg.smk
+++ b/spimquant/workflow/rules/templatereg.smk
@@ -127,9 +127,9 @@ rule crop_template:
     to the specified hemisphere region.
     """
     input:
-        template=bids_tpl(root=root, template="{template}", suffix="{suffix}.nii.gz"),
+        template=bids(root=root, template="{template}", suffix="{suffix}.nii.gz"),
     output:
-        cropped=bids_tpl(
+        cropped=bids(
             root=root,
             template="{template}",
             desc="{hemisphere}crop",
@@ -169,7 +169,7 @@ rule affine_reg:
         xfm_ras=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_="subject",
                 to="{template}",
                 type_="ras",
@@ -181,7 +181,7 @@ rule affine_reg:
         warped=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 space="{template}",
                 stain=stain_for_reg,
                 desc="affinewarped",
@@ -218,7 +218,7 @@ rule convert_ras_to_itk:
     input:
         xfm_ras=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_="subject",
             to="{template}",
             type_="ras",
@@ -230,7 +230,7 @@ rule convert_ras_to_itk:
         xfm_itk=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_="subject",
                 to="{template}",
                 type_="itk",
@@ -277,7 +277,7 @@ rule deform_reg:
         warp=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_="subject",
                 to="{template}",
                 suffix="warp.nii.gz",
@@ -287,7 +287,7 @@ rule deform_reg:
         invwarp=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 from_="{template}",
                 to="subject",
                 suffix="warp.nii.gz",
@@ -297,7 +297,7 @@ rule deform_reg:
         warped=temp(
             bids(
                 root=root,
-                datatype="warps",
+                datatype="xfm",
                 space="{template}",
                 stain=stain_for_reg,
                 desc="deformwarped",
@@ -351,7 +351,7 @@ rule compose_subject_to_template_warp:
     output:
         xfm_composite=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_="subject",
             to="{template}",
             suffix="xfm.nii.gz",
@@ -359,7 +359,7 @@ rule compose_subject_to_template_warp:
         ),
         xfm_composite_inv=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             from_="{template}",
             to="subject",
             suffix="xfm.nii.gz",
@@ -383,10 +383,8 @@ rule compose_subject_to_template_warp:
 rule resample_labels_to_zarr:
     """TODO: add required OME metadata"""
     input:
-        dseg=bids_tpl(root=root, template="{template}", desc="LR", suffix="dseg.nii.gz"),
-        label_tsv=bids_tpl(
-            root=root, template="{template}", desc="LR", suffix="dseg.tsv"
-        ),
+        dseg=bids(root=root, template="{template}", desc="LR", suffix="dseg.nii.gz"),
+        label_tsv=bids(root=root, template="{template}", desc="LR", suffix="dseg.tsv"),
         xfm_ras=rules.affine_reg.output.xfm_ras,
         zarr_zip=inputs["spim"].path,
     params:
@@ -586,16 +584,13 @@ rule deform_template_dseg_to_subject_nii:
             suffix="SPIM.nii.gz",
             **inputs["spim"].wildcards,
         ),
-        dseg=bids_tpl(
-            root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"
-        ),
+        dseg=bids(root=root, template="{template}", seg="{seg}", suffix="dseg.nii.gz"),
         xfm_composite_inv=rules.compose_subject_to_template_warp.output.xfm_composite_inv,
     output:
         dseg=bids(
             root=root,
-            datatype="micr",
+            datatype="parc",
             seg="{seg}",
-            desc="deform",
             level="{level}",
             from_="{template}",
             suffix="dseg.nii.gz",
@@ -614,34 +609,13 @@ rule deform_template_dseg_to_subject_nii:
         " -r {input.ref} -t {input.xfm_composite_inv}"
 
 
-rule copy_template_dseg_tsv:
-    input:
-        dseg=bids_tpl(root=root, template="{template}", seg="{seg}", suffix="dseg.tsv"),
-    output:
-        dseg=bids(
-            root=root,
-            datatype="micr",
-            seg="{seg}",
-            desc="deform",
-            level="{level}",
-            stain="{stain}",
-            from_="{template}",
-            suffix="dseg.tsv",
-            **inputs["spim"].wildcards,
-        ),
-    threads: 1
-    localrule: True
-    shell:
-        "cp {input} {output}"
-
-
 """ this rule needs updating - use atlas/seg wildcard and proper script
 rule deform_transform_labels_to_subj:
     input:
         ref_ome_zarr=inputs["spim"].path,
         xfm_ras=rules.affine_reg.output.xfm_ras,
         invwarp_nii=rules.deform_reg.output.invwarp,
-        flo_nii=bids_tpl(
+        flo_nii=bids(
             root=root, template="{template}", desc="LR", suffix="dseg.nii.gz"
         ),
     output:
@@ -661,7 +635,7 @@ rule deform_transform_labels_to_subj:
 
 rule transform_labels_to_zoomed_template:
     input:
-        dseg=bids_tpl(root=root, template="{template}", desc="LR", suffix="dseg.nii.gz"),
+        dseg=bids(root=root, template="{template}", desc="LR", suffix="dseg.nii.gz"),
         ref=bids(
             root=root,
             datatype="micr",
@@ -707,7 +681,7 @@ rule registration_qc_report:
         ),
         warped_affine=bids(
             root=root,
-            datatype="warps",
+            datatype="xfm",
             space="{template}",
             stain="{stain}",
             desc="affinewarped",
@@ -724,7 +698,7 @@ rule registration_qc_report:
             **inputs["spim"].wildcards,
         ),
         warp=rules.compose_subject_to_template_warp.output.xfm_composite,
-        dseg=lambda wildcards: bids_tpl(
+        dseg=lambda wildcards: bids(
             root=root,
             template=wildcards.template,
             seg=list(atlas_segs)[0],
@@ -733,9 +707,10 @@ rule registration_qc_report:
     output:
         report_html=bids(
             root=root,
-            datatype="micr",
+            datatype="xfm",
             stain="{stain}",
-            space="{template}",
+            from_="SPIM",
+            to="{template}",
             suffix="regqc.html",
             **inputs["spim"].wildcards,
         ),
diff --git a/spimquant/workflow/rules/vessels.smk b/spimquant/workflow/rules/vessels.smk
index f8ac72b..48b3d20 100644
--- a/spimquant/workflow/rules/vessels.smk
+++ b/spimquant/workflow/rules/vessels.smk
@@ -21,7 +21,7 @@ rule run_vesselfm:
     output:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="vessels",
             stain="{stain}",
             level="{level}",
             desc="vesselfm",
@@ -50,7 +50,7 @@ rule signed_distance_transform:
     input:
         mask=bids(
             root=root,
-            datatype="micr",
+            datatype="vessels",
             stain="{stain}",
             level="{level}",
             desc="vesselfm",
@@ -63,7 +63,7 @@ rule signed_distance_transform:
     output:
         dist=bids(
             root=root,
-            datatype="micr",
+            datatype="vessels",
             stain="{stain}",
             level="{level}",
             desc="{desc}",