diff --git a/pixi.lock b/pixi.lock
index 1d24a00..1d4be8b 100644
--- a/pixi.lock
+++ b/pixi.lock
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+- conda: https://conda.anaconda.org/conda-forge/noarch/werkzeug-3.1.4-pyhcf101f3_0.conda
+  sha256: 0c4a30a4713347ff822d73d2349fd9ef67a6f34993e7ae3434cdee7047e9ee1e
+  md5: de082192dffe45d19aff3d86a4d06a24
   depends:
   - markupsafe >=2.1.1
-  - python >=3.9
+  - python >=3.10
+  - python
   license: BSD-3-Clause
   license_family: BSD
   purls:
   - pkg:pypi/werkzeug?source=hash-mapping
-  size: 243546
-  timestamp: 1733160561258
+  size: 256621
+  timestamp: 1764423417723
 - conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_1.conda
   sha256: 1b34021e815ff89a4d902d879c3bd2040bc1bd6169b32e9427497fa05c55f1ce
   md5: 75cb7132eb58d97896e173ef12ac9986
@@ -13599,19 +15036,6 @@ packages:
   - pkg:pypi/wrapt?source=hash-mapping
   size: 64608
   timestamp: 1756851740646
-- conda: https://conda.anaconda.org/conda-forge/noarch/wslink-2.5.0-pyhd8ed1ab_0.conda
-  sha256: e9ac3caa3b17bed9bc301a67d3950f84fa37fb34002d2878c46cafb87978401d
-  md5: 8fa415e696acd9af59ce0a4425fd1b38
-  depends:
-  - aiohttp <4
-  - msgpack-python >=1,<2
-  - python >=3.10
-  license: BSD-3-Clause
-  license_family: BSD
-  purls:
-  - pkg:pypi/wslink?source=hash-mapping
-  size: 35839
-  timestamp: 1760984848678
 - conda: https://conda.anaconda.org/conda-forge/linux-64/x264-1!164.3095-h166bdaf_2.tar.bz2
   sha256: 175315eb3d6ea1f64a6ce470be00fa2ee59980108f246d3072ab8b977cb048a5
   md5: 6c99772d483f566d59e25037fea2c4b1
@@ -14063,20 +15487,20 @@ packages:
   - pkg:pypi/yarl?source=hash-mapping
   size: 151549
   timestamp: 1761337128623
-- conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.8.1-pyha770c72_1.conda
-  sha256: d07a11936266c89171033765e532531c668e6aa0f17bfc6839748f172bfb606e
-  md5: 79c2eed57446308ca2a0897ac58ba79d
+- conda: https://conda.anaconda.org/conda-forge/noarch/yte-1.9.4-pyhd8ed1ab_0.conda
+  sha256: 1ad021f32290e72b70a84dfe0c9b278c61aaa1254f1e1c287d68c32ee4f1093f
+  md5: 89d5edf5d52d3bc1ed4d7d3feef508ba
   depends:
-  - dpath
-  - plac
-  - python >=3.9
-  - pyyaml
+  - argparse-dataclass >=2.0.0,<3
+  - dpath >=2.1,<3.0
+  - python >=3.10
+  - pyyaml >=6.0,<7.0
   license: MIT
   license_family: MIT
   purls:
   - pkg:pypi/yte?source=hash-mapping
-  size: 15965
-  timestamp: 1763997913732
+  size: 16215
+  timestamp: 1764250734338
 - conda: https://conda.anaconda.org/conda-forge/linux-64/z5py-2.0.20-py312h473be34_2.conda
   sha256: 3d98fb402c95309754d9bfc1832ef01ecb38458106feb3d6cf463f7eddb77bcb
   md5: f2126332dc83c9a1e3d70727a87b7d91
@@ -14169,10 +15593,10 @@ packages:
   - pkg:pypi/zarr?source=hash-mapping
   size: 305998
   timestamp: 1763742695201
-- pypi: https://files.pythonhosted.org/packages/45/b8/b5220d848461c15609bdd7eafa86119bb5cc606d3cf8ca15921e5587ec7c/zarrnii-0.14.0a1-py3-none-any.whl
+- pypi: ./zarrnii
   name: zarrnii
-  version: 0.14.0a1
-  sha256: 62908be04baa838b82e741a164df9324945321d472386a49262fe67bda649e15
+  version: 0.14.0a2.dev0
+  sha256: 07d0a0402ad1befae98302092d097a0ce59eb9846d5bd90f78fac3c9b844421e
   requires_dist:
   - dask>=2025.5.1
   - h5py>=3.14.0
@@ -14206,6 +15630,7 @@ packages:
   - antspyx>=0.5.0 ; extra == 'n4'
   - templateflow>=0.8.0 ; extra == 'templateflow'
   requires_python: '>=3.11,<3.14'
+  editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h387f397_9.conda
   sha256: 47cfe31255b91b4a6fa0e9dbaf26baa60ac97e033402dbc8b90ba5fee5ffe184
   md5: 8035e5b54c08429354d5d64027041cad
@@ -14250,17 +15675,18 @@ packages:
   - pkg:pypi/zict?source=hash-mapping
   size: 36341
   timestamp: 1733261642963
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhd8ed1ab_0.conda
-  sha256: 7560d21e1b021fd40b65bfb72f67945a3fcb83d78ad7ccf37b8b3165ec3b68ad
-  md5: df5e78d904988eb55042c0c97446079f
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
+  sha256: b4533f7d9efc976511a73ef7d4a2473406d7f4c750884be8e8620b0ce70f4dae
+  md5: 30cd29cb87d819caead4d55184c1d115
   depends:
-  - python >=3.9
+  - python >=3.10
+  - python
   license: MIT
   license_family: MIT
   purls:
-  - pkg:pypi/zipp?source=hash-mapping
-  size: 22963
-  timestamp: 1749421737203
+  - pkg:pypi/zipp?source=compressed-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
@@ -14273,9 +15699,9 @@ packages:
   purls: []
   size: 92286
   timestamp: 1727963153079
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.2.5-hde8ca8f_0.conda
-  sha256: 3a8e7798deafd0722b6b5da50c36b7f361a80b30165d600f7760d569a162ff95
-  md5: 1920c3502e7f6688d650ab81cd3775fd
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.2.5-hde8ca8f_1.conda
+  sha256: 84ea17cb646d8a916d9335415f57c9e5dd001de158972322c714ebe1b72670b0
+  md5: c860578a89dc9b6003d600181612287c
   depends:
   - __glibc >=2.17,<3.0.a0
   - libgcc >=14
@@ -14283,8 +15709,19 @@ packages:
   license: Zlib
   license_family: Other
   purls: []
-  size: 110843
-  timestamp: 1754587144298
+  size: 110969
+  timestamp: 1764162891322
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.3.2-h54a6638_0.conda
+  sha256: 0afb07f3511031c35202036e2cd819c90edaa0c6a39a7a865146d3cb066bec96
+  md5: 0faadd01896315ceea58bcc3479b1d21
+  depends:
+  - libgcc >=14
+  - __glibc >=2.17,<3.0.a0
+  - libstdcxx >=14
+  license: Zlib
+  purls: []
+  size: 135032
+  timestamp: 1764715875371
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.25.0-py312h5253ce2_1.conda
   sha256: c2bcb8aa930d6ea3c9c7a64fc4fab58ad7bcac483a9a45de294f67d2f447f413
   md5: 02738ff9855946075cbd1b5274399a41
@@ -14319,16 +15756,13 @@ packages:
   - pkg:pypi/zstandard?source=hash-mapping
   size: 471496
   timestamp: 1762512679097
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
-  sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
-  md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+  sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
+  md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
   depends:
   - __glibc >=2.17,<3.0.a0
-  - libgcc >=13
-  - libstdcxx >=13
   - libzlib >=1.3.1,<2.0a0
   license: BSD-3-Clause
-  license_family: BSD
   purls: []
-  size: 567578
-  timestamp: 1742433379869
+  size: 601375
+  timestamp: 1764777111296
diff --git a/pyproject.toml b/pyproject.toml
index db71f7f..8a0c093 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,6 +12,7 @@ requires = ["hatchling"]
 [tool.pixi.workspace]
 channels = ["conda-forge", "bioconda"]
 platforms = ["linux-64"]
+preview = ["pixi-build"]
 
 [tool.pixi.feature.runtime.dependencies]
 snakemake = ">=9.5.1,<10"
@@ -27,7 +28,6 @@ conda = ">=25.5.0,<26"
 snakemake-executor-plugin-slurm = ">=1.4.0,<2"
 snakemake-storage-plugin-fs = ">=1.1.2,<2"
 snakemake-storage-plugin-http = ">=0.3.0,<0.4.0"
-greedyreg = "==0.0.20250712"
 antspyx = "==0.6.1"
 markdown-it-py = "<4"
 docutils = "<0.22"
@@ -35,9 +35,9 @@ docutils = "<0.22"
 [tool.pixi.pypi-dependencies]
 spimquant = { path = ".", editable = true }
 ngff-zarr = { version = ">=0.19.1", extras = ["cli","dask-image","itk","tensorstore","validate"] }
-zarrnii = ">=0.14.0-alpha1,<0.15.0"
+#zarrnii = ">=0.14.0-alpha1,<0.15.0"
 #zarrnii = { git = "https://github.com/khanlab/zarrnii", rev = "v0.13.0-alpha1",  editable = true }
-#zarrnii = { path = "./zarrnii", editable = true }
+zarrnii = { path = "./zarrnii", editable = true }
 
 [tool.pixi.feature.dev.dependencies]
 black   = ">=24.0.0, <25.0.0"
@@ -51,10 +51,23 @@ jupyterlab = ">=4.4.7,<5"
 napari = ">=0.6.6,<0.7"
 napari-ome-zarr = ">=0.6.1,<0.7"
 pyqt = ">=5.15.11,<6"
+jupyterlab = ">=4.4.10,<5"
+seaborn = ">=0.13.2,<0.14"
+
+[tool.pixi.feature.experimental.dependencies]
 micro_sam = ">=1.6.2,<2"
+cellpose = ">=4.0.7,<5"
+
+
+[tool.pixi.feature.stardist.dependencies]
+tensorflow = "*"
+
+[tool.pixi.feature.stardist.pypi-dependencies]
+stardist = { path = "/local/scratch/stardist", editable = true }
+
 
 [tool.pixi.environments.default]
-features = ["runtime"]
+features = ["runtime","stardist"]
 
 [tool.pixi.environments.dev]
 features = ["runtime", "dev", "vis"]
@@ -63,10 +76,14 @@ features = ["runtime", "dev", "vis"]
 [tool.pixi.environments.dev-only]
 features = ["dev"]
 
+[tool.pixi.environments.experimental]
+features = ["runtime","vis","experimental"]
+
+
+
+
 [tool.pixi.tasks]
 quality_check = "isort --profile black spimquant/*.py -c && black spimquant --check && snakefmt spimquant --check"
 quality_fix = "isort --profile black spimquant/*.py && black spimquant  && snakefmt spimquant"
 
-[tool.pixi.dependencies]
-jupyterlab = ">=4.4.10,<5"
-pip = ">=25.3,<26"
+
diff --git a/spimquant/config/snakebids.yml b/spimquant/config/snakebids.yml
index aaceb07..09edee3 100644
--- a/spimquant/config/snakebids.yml
+++ b/spimquant/config/snakebids.yml
@@ -302,4 +302,8 @@ seg_metrics:
   - count
   - volume
   - nvoxels
+  - equivdiameter
 
+stardist:
+  model_urls:
+    3D_demo: https://github.com/stardist/stardist-models/releases/download/v0.1/python_3D_demo.zip
diff --git a/spimquant/workflow/Snakefile b/spimquant/workflow/Snakefile
index 4200377..e185edb 100644
--- a/spimquant/workflow/Snakefile
+++ b/spimquant/workflow/Snakefile
@@ -299,7 +299,7 @@ include: "rules/masking.smk"
 include: "rules/templatereg.smk"
 include: "rules/segmentation.smk"
 include: "rules/patches.smk"
-
+include: "rules/stardist.smk"
 
 if config["register_to_mri"]:
 
diff --git a/spimquant/workflow/envs/greedy.yaml b/spimquant/workflow/envs/greedy.yaml
new file mode 100644
index 0000000..de5cae6
--- /dev/null
+++ b/spimquant/workflow/envs/greedy.yaml
@@ -0,0 +1,5 @@
+name: greedy
+channels:
+  - conda-forge
+dependencies:
+  - greedyreg=0.0.20250712
diff --git a/spimquant/workflow/envs/stardist.yaml b/spimquant/workflow/envs/stardist.yaml
new file mode 100644
index 0000000..e98f213
--- /dev/null
+++ b/spimquant/workflow/envs/stardist.yaml
@@ -0,0 +1,13 @@
+name: stardist
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - stardist=0.9.1
+  - dask
+  - zarr
+  - pip
+  - pip:
+    - zarrnii
+
diff --git a/spimquant/workflow/rules/masking.smk b/spimquant/workflow/rules/masking.smk
index 554e2ad..260c503 100644
--- a/spimquant/workflow/rules/masking.smk
+++ b/spimquant/workflow/rules/masking.smk
@@ -189,6 +189,7 @@ rule init_affine_reg:
     resources:
         mem_mb=16000,
         runtime=5,
+    conda: "../envs/greedy.yaml"
     shell:
         "greedy -threads {threads} -d 3 -i {input.template} {input.subject} "
         " -a -dof 12 -ia-image-centers -m NMI -o {output.xfm_ras} -n {params.iters} && "
@@ -226,6 +227,7 @@ rule affine_transform_template_mask_to_subject:
     resources:
         mem_mb=16000,
         runtime=5,
+    conda: "../envs/greedy.yaml"
     shell:
         " greedy -threads {threads} -d 3 -rf {input.ref} "
         " -ri NN"
diff --git a/spimquant/workflow/rules/preproc_mri.smk b/spimquant/workflow/rules/preproc_mri.smk
index db0cb69..d6bd93c 100644
--- a/spimquant/workflow/rules/preproc_mri.smk
+++ b/spimquant/workflow/rules/preproc_mri.smk
@@ -124,6 +124,7 @@ rule rigid_greedy_reg_mri_to_template:
     resources:
         mem_mb=16000,
         runtime=15,
+    conda: "../envs/greedy.yaml"
     shell:
         "greedy -threads {threads} -d 3 -i {input.template} {input.subject} "
         " -a -dof 6 -ia-image-centers -m {params.metric} -o {output.xfm_ras} && "
@@ -274,6 +275,7 @@ rule apply_mri_brain_mask:
     resources:
         mem_mb=16000,
         runtime=15,
+    conda: "../envs/c3d.yaml"
     shell:
         "c3d {input.nii} {input.mask} -multiply -resample 300% -o {output.nii}"
 
@@ -383,6 +385,7 @@ rule rigid_greedy_reg_mri_to_spim:
     resources:
         mem_mb=16000,
         runtime=15,
+    conda: "../envs/greedy.yaml"
     shell:
         "greedy -threads {threads} -d 3 -i {input.spim} {input.mri} "
         " -a -dof {params.dof} -ia-image-centers -m {params.metric_rigid} -o {output.xfm_ras} && "
@@ -507,6 +510,7 @@ rule warp_mri_to_template_via_spim:
     resources:
         mem_mb=16000,
         runtime=15,
+    conda: "../envs/greedy.yaml"
     shell:
         " greedy -threads {threads} -d 3 -rf {input.ref} "
         "  -rm {input.mri} {output.warped} "
@@ -587,6 +591,7 @@ rule warp_mri_brainmask_to_spim:
     resources:
         mem_mb=16000,
         runtime=15,
+    conda: "../envs/greedy.yaml"
     shell:
         " greedy -threads {threads} -d 3 -rf {input.ref} -ri NN"
         "  -rm {input.mask} {output.mask} "
diff --git a/spimquant/workflow/rules/segmentation.smk b/spimquant/workflow/rules/segmentation.smk
index 34c0e92..2fe0023 100644
--- a/spimquant/workflow/rules/segmentation.smk
+++ b/spimquant/workflow/rules/segmentation.smk
@@ -387,6 +387,7 @@ rule deform_negative_mask_to_subject_nii:
     resources:
         mem_mb=16000,
         runtime=15,
+    conda: "../envs/greedy.yaml"
     shell:
         " greedy -threads {threads} -d 3 -rf {input.ref} "
         " -ri NN "
diff --git a/spimquant/workflow/rules/stardist.smk b/spimquant/workflow/rules/stardist.smk
new file mode 100644
index 0000000..d2146b5
--- /dev/null
+++ b/spimquant/workflow/rules/stardist.smk
@@ -0,0 +1,59 @@
+rule get_model:
+    input:
+        model_zip=lambda wildcards: storage(config['stardist']['model_urls'][wildcards.model_name])
+    output:
+        model_dir=directory('resources/stardist_models/{model_name}')
+    shell:
+        'unzip -d {output.model_dir} {input.model_zip}'
+        
+rule test_stardist:
+    input:
+        model_dir=directory('resources/stardist_models/3D_demo')
+    output:
+        out_dir=directory('test_stardist')
+    script: '../scripts/test_stardist.py'
+
+rule segment_stardist:
+    input:
+        spim=inputs["spim"].path,
+    params:
+        zarrnii_kwargs=lambda wildcards: {"orientation": config["orientation"],channel_labels=[wildcards.stain]},
+    output:
+        regionprops=temp(
+            directory(
+                bids(
+                    root=work,
+                    datatype="micr",
+                    stain="{stain}",
+                    level="{level}",
+                    desc="correctedn4",
+                    suffix="SPIM.ome.zarr",
+                    **inputs["spim"].wildcards,
+                )
+            )
+        ),
+        biasfield=temp(
+            directory(
+                bids(
+                    root=work,
+                    datatype="micr",
+                    stain="{stain}",
+                    level="{level}",
+                    desc="n4",
+                    suffix="biasfield.ome.zarr",
+                    **inputs["spim"].wildcards,
+                )
+            )
+        ),
+    group:
+        "subj"
+    threads: 128
+    resources:
+        mem_mb=500000,
+        disk_mb=2097152,
+        runtime=60,
+    script:
+        "../scripts/n4_biasfield.py"
+
+
+
diff --git a/spimquant/workflow/rules/templatereg.smk b/spimquant/workflow/rules/templatereg.smk
index 66d664f..5ab56a7 100644
--- a/spimquant/workflow/rules/templatereg.smk
+++ b/spimquant/workflow/rules/templatereg.smk
@@ -162,6 +162,7 @@ rule affine_reg:
     resources:
         mem_mb=16000,
         runtime=5,
+    conda: "../envs/greedy.yaml"
     shell:
         "greedy -threads {threads} -d 3 -i {input.template} {input.subject} "
         " -a -dof 12 -ia-image-centers -m NMI -o {output.xfm_ras} -n {params.iters} && "
@@ -265,6 +266,7 @@ rule deform_reg:
     resources:
         mem_mb=16000,
         runtime=5,
+    conda: "../envs/greedy.yaml"
     shell:
         "greedy -threads {threads} -d 3 -i {input.template} {input.subject} "
         " -it {input.xfm_ras} -m {params.metric} "
diff --git a/spimquant/workflow/scripts/test_stardist.py b/spimquant/workflow/scripts/test_stardist.py
new file mode 100644
index 0000000..ce15d38
--- /dev/null
+++ b/spimquant/workflow/scripts/test_stardist.py
@@ -0,0 +1,43 @@
+if __name__ == "__main__":
+
+    from dask.distributed import Client, LocalCluster
+
+    cluster = LocalCluster(
+        n_workers=int(snakemake.threads / 2),  # or 32, depending on workload
+        threads_per_worker=2,  # isolate GIL
+        memory_limit="auto",  # or tune to your RAM
+        dashboard_address=":8788",
+    )
+    client = Client(cluster)
+    print(cluster.dashboard_link)
+
+
+    from zarrnii import ZarrNii
+
+    import zarrnii
+    znimg = ZarrNii.from_ome_zarr('/nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3/bids/sub-AS134F1/micr/sub-AS134F1_sample-brain_acq-imaris4x_SPIM.ome.zarr')
+    print(znimg)
+
+    import nibabel as nib
+    import numpy as np
+    from stardist.models import StarDist3D
+    from csbdeep.utils import normalize
+    from stardist.data import test_image_nuclei_3d
+    from pathlib import Path
+
+
+    model = StarDist3D(None, name=snakemake.input.model_dir)
+
+    img = test_image_nuclei_3d()
+
+
+
+    labels,_ = model.predict_instances(normalize(img))
+
+
+    out_dir_path = Path(snakemake.output.out_dir)
+    out_dir_path.mkdir()
+
+    nib.Nifti1Image(img,affine=np.eye(4,4)).to_filename(out_dir_path / 'img.nii')
+    nib.Nifti1Image(labels,affine=np.eye(4,4)).to_filename(out_dir_path / 'labels.nii')
+