diff --git a/.gitignore b/.gitignore
index 1df552c..73a8409 100755
--- a/.gitignore
+++ b/.gitignore
@@ -171,4 +171,7 @@ cython_debug/
 pdm.toml
 
 #csv
-*.csv
\ No newline at end of file
+*.csv
+
+#mesh temporary director
+emt_tmp/
\ No newline at end of file
diff --git a/EMT_data_analysis/analysis_scripts/Analysis_tools.py b/EMT_data_analysis/analysis_scripts/Analysis_tools.py
index 96744ff..ffbd77e 100644
--- a/EMT_data_analysis/analysis_scripts/Analysis_tools.py
+++ b/EMT_data_analysis/analysis_scripts/Analysis_tools.py
@@ -88,6 +88,7 @@ def load_io_data(df):
     ]]
 
     df_io = io.load_inside_outside_classification()
+    df_io = df_io[df_io['Z']<27]
 
     dfio_merged=pd.merge(df_io, df_info, on='Data ID', suffixes=['','_remove'])
     remove = [col for col in dfio_merged.columns if 'remove' in col]
diff --git a/EMT_data_analysis/analysis_scripts/Feature_extraction.py b/EMT_data_analysis/analysis_scripts/Feature_extraction.py
index 94ec594..5bd26b4 100755
--- a/EMT_data_analysis/analysis_scripts/Feature_extraction.py
+++ b/EMT_data_analysis/analysis_scripts/Feature_extraction.py
@@ -38,7 +38,7 @@ def compute_bf_colony_features_all_movies(output_folder, align=True):
         print(f"Movie: {movie_id}")
         
         print("Getting raw data...")
-        raw_path = df_movie["File URL"].values[0]
+        raw_path = df_movie["Raw File URL"].values[0]
         raw_reader = BioImage(raw_path)
         print(raw_path)
         print(raw_reader.shape)
diff --git a/EMT_data_analysis/analysis_scripts/Nuclei_localization.py b/EMT_data_analysis/analysis_scripts/Nuclei_localization.py
index 5c8b682..0d62333 100755
--- a/EMT_data_analysis/analysis_scripts/Nuclei_localization.py
+++ b/EMT_data_analysis/analysis_scripts/Nuclei_localization.py
@@ -11,7 +11,6 @@
 import pyvista as pv
 import trimesh
 import point_cloud_utils as pcu
-import pymeshfix as mf
 
 from bioio import BioImage
 
@@ -25,7 +24,7 @@
 
 def nuclei_localization(
         df:pd.DataFrame, 
-        movie_id:str,
+        data_id:str,
         output_directory:str,
         align_segmentation:bool=True,
     ):
@@ -36,8 +35,8 @@ def nuclei_localization(
         ----------
         manifest_path: str
             Path to the csv manifest of the full dataset
-        movie_id: str
-            Movie ID from manifest for data to process
+        data_id: str
+            Data ID from manifest for data to process
         output_directory: str
             Path to the output directory where the localized nuclei data will be saved.
         align_segmentation: bool
@@ -57,7 +56,7 @@ def nuclei_localization(
     elif df['Gene'].values[0] == 'EOMES|TBR2':
         seg_path = df['EOMES Nuclear Segmentation URL'].values[0]
     else:
-        raise ValueError(f"The move {movie_id} does not have EOMES or H2B segmentations")
+        raise ValueError(f"The move {data_id} does not have EOMES or H2B segmentations")
         
     # import pdb; pdb.set_trace()
     segmentations = BioImage(df['CollagenIV Segmentation Probability URL'].values[0])
@@ -77,7 +76,7 @@ def nuclei_localization(
     # localize nuclei for each timepoint
     num_timepoints = int(df['Image Size T'].values[0])
     nuclei = []
-    for timepoint in tqdm(range(num_timepoints), desc=f"Movie {movie_id}"):
+    for timepoint in tqdm(range(num_timepoints), desc=f"Movie {data_id}"):
         # check if mesh exists for this timepoint
         if f'{timepoint}' not in meshes.keys():
             print(f"Mesh for timepoint {timepoint} not found.")
@@ -87,7 +86,7 @@ def nuclei_localization(
             break
         
         if align_segmentation:
-            alignment_matrix = alignment.parse_rotation_matrix_from_string(df['Camera Alignment Matrix'].values[0])
+            alignment_matrix = alignment.parse_rotation_matrix_from_string(df['Dual Camera Alignment Matrix Value'].values[0])
         else:
             alignment_matrix = np.zeros((3,3))
 
@@ -99,7 +98,7 @@ def nuclei_localization(
             alignment_matrix=alignment_matrix
         )
         
-        nuclei_tp['Movie ID'] = movie_id
+        nuclei_tp['Data ID'] = data_id
         nuclei_tp['Time hr'] = timepoint / 0.5
         nuclei.append(nuclei_tp)
         
@@ -110,7 +109,7 @@ def nuclei_localization(
     newcols.extend(cols[:-2])
     nuclei = nuclei[newcols]
 
-    out_fn = out_dir / (movie_id + "_localized_nuclei.csv")
+    out_fn = out_dir / (data_id + "_localized_nuclei.csv")
     nuclei.to_csv(out_fn, index=False)
     rmtree(tmp_dir)
 
@@ -230,8 +229,8 @@ def run_nuclei_localization(
         ----------
         manifest_path: str
             Path to the csv manifest of the full dataset
-        movie_id: str
-            Movie ID from manifest for data to process
+        data_id: str
+            Data ID from manifest for data to process
         output_directory: str
             Path to the output directory where the localized nuclei data will be saved.
         align_segmentation: bool
@@ -244,13 +243,13 @@ def run_nuclei_localization(
 
     print(f"Processing {len(df_cond)} movies with CollagenIV segmentations.")
 
-    for movie_id in tqdm(pd.unique(df_cond['Movie ID']), desc="Movies"):
-        df_id = df_manifest[df_manifest['Movie ID'] == movie_id]
+    for data_id in tqdm(pd.unique(df_cond['Data ID']), desc="Movies"):
+        df_id = df_manifest[df_manifest['Data ID'] == data_id]
 
         # make sure the movie has the required segmentations
         nuclei_localization(
             df=df_id,
-            movie_id=movie_id,
+            data_id=data_id,
             output_directory=output_directory,
             align_segmentation=align_segmentation
         )
diff --git a/EMT_data_analysis/figure_generation/colony_mask.py b/EMT_data_analysis/figure_generation/colony_mask.py
index f864e16..c861a09 100755
--- a/EMT_data_analysis/figure_generation/colony_mask.py
+++ b/EMT_data_analysis/figure_generation/colony_mask.py
@@ -14,12 +14,10 @@
 from skimage.morphology import remove_small_objects
 import argparse
 from typing import List
-
+from EMT_data_analysis.tools import io, const
 
 def main(
-        dataset_manifest_path: str,
-        colony_feature_manifest_path: str,
-        movie_id: str,
+        data_id: str,
         out_dir: str,
     ):
     '''
@@ -27,24 +25,26 @@ def main(
         
         Parameters
         ----------
-        dataset_manifest_path: str
-            Path to the csv manifest containing summary data of the entire dataset
-        colony_feature_manifest_path: str
-            Path to the csv manifest containing results from brightfield colony mask feature extraction.
-        movie_id: str
-            Movie Unique ID of the movie.
+        data_id: str
+            Data ID of the movie.
         out_dir: str
             Path to the output directory where the visualization will be saved.
     '''
+
+    if out_dir is None:
+        out_dir = io.setup_base_directory_name("figures/3D Renders")
+    else:
+        out_dir = Path(out_dir)
+        out_dir.mkdir(exist_ok=True, parents=True)
     
     # get bottom z layer
-    df_feature = pd.read_csv(colony_feature_manifest_path)
-    zbottom = df_feature.loc[df['Movie Unique ID'] == movie_id, 'z_bottom'].values[0]
+    df_feature = io.load_image_analysis_extracted_features()
+    zbottom = int(df_feature.loc[df_feature['Data ID'] == data_id, 'Bottom Z plane'].values[0])
     
     # get segmentation and base filename
-    df_manifest = pd.read_csv(dataset_manifest_path)
-    seg_fn = df_manifest.loc[df_manifest['Movie Unique ID'] == movie_id, 'All Cells Mask File Download'].values[0]
-    seg = BioIo(seg_fn)
+    df_manifest = io.load_imaging_and_segmentation_dataset()
+    seg_fn = df_manifest.loc[df_manifest['Data ID'] == data_id, 'All Cells Mask File Download'].values[0]
+    seg_file = BioImage(seg_fn)
     outname = Path(seg_fn).stem + '_figure'
     
     # lighting setup
@@ -65,6 +65,7 @@ def main(
     )
 
     # process frames for 0, 16, 32, and 48 hours
+    pv.start_xvfb()
     pl = pv.Plotter(off_screen=True, notebook=False, window_size=(1088, 1088))
     for tp in tqdm([0, 32, 64, 96]):
         # clear scene
@@ -231,30 +232,21 @@ def cgal_vertices_faces_triangle_mesh(Q: Polyhedron_3):
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Generate figures for colony mask segmentation.')
 
+    
     parser.add_argument(
-        '--manifest_path',
-        type=str,
-        required=True,
-        help='Path to the csv manifest containing summary data of the entire dataset.'
-    )
-    parser.add_argument(
-        '--feature_path',
-        type=str,
-        required=True,
-        help='Path to the csv manifest containing results from brightfield colony mask feature extraction.'
-    )
-    parser.add_argument(
-        '--movie_id',
+        '--data_id',
         type=str,
-        required=True,
         help='Movie Unique ID of the movie.'
     )
     parser.add_argument(
         '--output_directory',
         type=str,
-        required=True,
         help='Path to the output directory where the visualization will be saved.'
     )
 
     args = parser.parse_args()
-    main(args.manifest_path, args.feature_path, args.movie_id, args.output_directory)
+    if args.data_id is None:
+        for data_id in const.EXAMPLE_ACM_IDS:
+            main(data_id, args.output_directory)
+    else:
+        main(args.data_id, args.output_directory)
diff --git a/EMT_data_analysis/figure_generation/inside-outside_classification.py b/EMT_data_analysis/figure_generation/inside-outside_classification.py
index aa4b2ee..2fd1465 100755
--- a/EMT_data_analysis/figure_generation/inside-outside_classification.py
+++ b/EMT_data_analysis/figure_generation/inside-outside_classification.py
@@ -11,13 +11,14 @@
 import pandas as pd
 import argparse
 import quilt3 as q3
+from typing import Optional
 
-from EMT_data_analysis.tools import alignment, io
+from EMT_data_analysis.tools import alignment, io, const
 
 
 def main(
-        data_id: str,
-        output: str
+        data_id: Optional[str]=None,
+        output: Optional[str]=None
     ):
     '''
         Generate three figures for the inside-outside classification of nuclei
@@ -25,24 +26,28 @@ def main(
         
         Parameters
         ----------
-        mesh_fn: str
-            Path to the .vtm file for the whole colony timelapse.
-        mid: str
+        data_id: str
             Data ID of the movie.
-        data_csv: str
-            Path to the CSV file containing the inside-outside classification data.
         output: str
             Path to the output directory where the figures will be saved.
     '''
     # ensure output directory exists
-    output = Path(output)
-    output.mkdir(exist_ok=True, parents=True)
+
+    if data_id is None:
+        data_id = const.EXAMPLE_IO_ID
+
+    if output is None:
+        output = io.setup_base_directory_name("figures/Inside-Outside/mesh-figures")
+    else:
+        output = Path(output)
+        output.mkdir(exist_ok=True, parents=True)
     
     # load data
     df_meta = io.load_imaging_and_segmentation_dataset()
     df_meta = df_meta[df_meta['Data ID'] == data_id]
     df = io.load_inside_outside_classification()
     df = df[df['Data ID'] == data_id]
+    df = df[df['Z']<27]
 
     tmp_dir = Path("./emt_tmp/nuclei_localization/")
     tmp_dir.mkdir(exist_ok=True, parents=True)
@@ -146,14 +151,12 @@ def create_nucleus_mesh(df_nucleus: pd.DataFrame):
     parser = argparse.ArgumentParser(description='Generate figures for inside-outside classification of nuclei.')
     parser.add_argument(
         '--data_id', 
-        type=str, 
-        default='3500005828_45',
-        help='FMS ID of the movie.'
+        type=str,
+        help='Data ID of the movie.'
     )
     parser.add_argument(
         '--output', 
         type=str,
-        required=True,
         help='Path to the output directory where the figures will be saved.'
     )
     
diff --git a/EMT_data_analysis/tools/const.py b/EMT_data_analysis/tools/const.py
index 23d4060..7ac45f2 100644
--- a/EMT_data_analysis/tools/const.py
+++ b/EMT_data_analysis/tools/const.py
@@ -42,4 +42,10 @@
     '3500005834_55']
 
 # Nuclues Fraction Inside/Outside Example
-EXAMPLE_IO_ID = '3500005828_45'
\ No newline at end of file
+EXAMPLE_IO_ID = '3500005828_45'
+
+# All Cells Mask Examples
+EXAMPLE_ACM_IDS = [
+    '3500005824_36',
+    '3500006256_12'
+]
\ No newline at end of file
diff --git a/README.md b/README.md
index 98b73cf..ea892db 100755
--- a/README.md
+++ b/README.md
@@ -24,27 +24,55 @@ pip install -e .
 
 ## 1 - Feature extraction
 
-Run: `python Feature_extraction.py`
+Run: `python EMT_data_analysis/analysis_scripts/Feature_extraction.py`
 
 This will generate one CSV for each movie with the extracted features. CSVs are stored in the folder `EMT_data_analysis/results/feature_extraction`
 
 ## 2 - Metric computation
 
-Run: `python Metric_computation.py`
+Run: `python EMT_data_analysis/analysis_scripts/Metric_computation.py`
 
 This will generate a single CSV containing information about all the movies to be used for analysis. The manifest is saved as `EMT_data_analysis/results/metric_computation/Image_analysis_extracted_features.csv`.
 
 ## 3 - Nuclei localization
 
-Run: `python Nuclei_localization.py`
+Run: `python EMT_data_analysis/analysis_scripts/Nuclei_localization.py`
 
 This will generate CSV for individual nuclei classified as inside the basement memebrane or not over the course of the timelapse for EOMES and H2B movies. The manifest is saved as `EMT_data_analysis/results/nuclei_localization/Migration_timing_trough_mesh_extracted_feature.csv`.
 
 ## 4 - Analysis Plots
 
-Run: `python Analysis_tools.py`
+Run: `python EMT_data_analysis/analysis_scripts/Analysis_tools.py`
+
+This will generate the plots in the manuscript and store them in `results/figures` folder. The manifests used as inputs in this workflow are automatically downloaded from [AWS](https://open.quiltdata.com/b/allencell/tree/aics/emt_timelapse_dataset/manifests/) by default. 
+
+## 5 - [Optional] 3D Example Rendering
+
+The functions in `EMT_data_analysis/figure_generation` can be used to generate 3D renderings shown in the paper. Functions have only been tested on Ubuntu 18.04/22.04
+
+On Ubuntu or Debian:
+```bash
+sudo apt-get install xvfb libgl1-mesa-glx
+```
+On Windows: 
+Comment out any instance of `pv.start_xvfb()` in the code before running.
+
+### All Cells Mask
+Run
+```bash
+python EMT_data_analysis/figure_generation/colony_mask.py --data_id [Optional] --output_directory [Optional]
+```
+If no input arguments are provided, the code will default to the data shown in the paper and output results to `EMT_data_analysis/results/3D_all_cells_mask`.
+Data ID values are only valid inputs if they have a none-empty value for `All Cells Mask File Download` in the `image_and_segmentation_data.csv` manifest on [AWS](https://open.quiltdata.com/b/allencell/tree/aics/emt_timelapse_dataset/manifests/)
+
+### Inside-Outside Classification
+Run
+```bash
+python EMT_data_analysis/figure_generation/inside-outside_classification.py --data_id [Optional] --output_directory [Optional]
+```
+If no input arguments are provided, the code will default to the data shown in the paper and output results to `EMT_data_analysis/results/Inside-Outside/mesh-figures`.
+Data ID values are only valid inputs if they have a none-empty value for `CollagenIV Segmentation Mesh Folder` in the `image_and_segmentation_data.csv` manifest on [AWS](https://open.quiltdata.com/b/allencell/tree/aics/emt_timelapse_dataset/manifests/)
 
-This will generate the plots in the manuscript and store them in `results/figures` folder. The manifests used as inputs in this workflow are automatically downloaded from [AWS](https://open.quiltdata.com/b/allencell/tree/aics/emt_timelapse_dataset/manifests/) by default. The user can opt to also use local version of these manifests if they produced locally by running the scripts `Feature_extraction.py`, `Metric_computation.py` and `Nuclei_localization.py`. To use local version of the manifests, please set `load_from_aws=False` everywhere in the script `Analysis_plots.py`.
 
 # Contact
 If you have questions about this code, please reach out to us at cells@alleninstitute.org.
diff --git a/pdm.lock b/pdm.lock
index d3d35c1..42ac16b 100644
--- a/pdm.lock
+++ b/pdm.lock
@@ -3,18 +3,39 @@
 
 [metadata]
 groups = ["default", "internal"]
-strategy = []
+strategy = ["inherit_metadata"]
 lock_version = "4.5.0"
-content_hash = "sha256:cb2bc908479b143cda2386f4f117a3b1b82814b0341f8e9a5689ba5c791f8d2a"
+content_hash = "sha256:5f64c6a03611318ab5cd1db24294e634d1ce935963ad49c918b01d4d462c60b4"
 
 [[metadata.targets]]
 requires_python = ">=3.11,<3.12"
 
+[[package]]
+name = "aiobotocore"
+version = "2.25.1"
+requires_python = ">=3.9"
+summary = "Async client for aws services using botocore and aiohttp"
+groups = ["default"]
+dependencies = [
+    "aiohttp<4.0.0,>=3.9.2",
+    "aioitertools<1.0.0,>=0.5.1",
+    "botocore<1.40.62,>=1.40.46",
+    "jmespath<2.0.0,>=0.7.1",
+    "multidict<7.0.0,>=6.0.0",
+    "python-dateutil<3.0.0,>=2.1",
+    "wrapt<2.0.0,>=1.10.10",
+]
+files = [
+    {file = "aiobotocore-2.25.1-py3-none-any.whl", hash = "sha256:eb6daebe3cbef5b39a0bb2a97cffbe9c7cb46b2fcc399ad141f369f3c2134b1f"},
+    {file = "aiobotocore-2.25.1.tar.gz", hash = "sha256:ea9be739bfd7ece8864f072ec99bb9ed5c7e78ebb2b0b15f29781fbe02daedbc"},
+]
+
 [[package]]
 name = "aiohttp"
 version = "3.9.5"
 requires_python = ">=3.8"
 summary = "Async http client/server framework (asyncio)"
+groups = ["default"]
 dependencies = [
     "aiosignal>=1.1.2",
     "async-timeout<5.0,>=4.0; python_version < \"3.11\"",
@@ -87,11 +108,26 @@ files = [
     {file = "aiohttp-3.9.5.tar.gz", hash = "sha256:edea7d15772ceeb29db4aff55e482d4bcfb6ae160ce144f2682de02f6d693551"},
 ]
 
+[[package]]
+name = "aioitertools"
+version = "0.13.0"
+requires_python = ">=3.9"
+summary = "itertools and builtins for AsyncIO and mixed iterables"
+groups = ["default"]
+dependencies = [
+    "typing-extensions>=4.0; python_version < \"3.10\"",
+]
+files = [
+    {file = "aioitertools-0.13.0-py3-none-any.whl", hash = "sha256:0be0292b856f08dfac90e31f4739432f4cb6d7520ab9eb73e143f4f2fa5259be"},
+    {file = "aioitertools-0.13.0.tar.gz", hash = "sha256:620bd241acc0bbb9ec819f1ab215866871b4bbd1f73836a55f799200ee86950c"},
+]
+
 [[package]]
 name = "aiosignal"
 version = "1.3.1"
 requires_python = ">=3.7"
 summary = "aiosignal: a list of registered asynchronous callbacks"
+groups = ["default"]
 dependencies = [
     "frozenlist>=1.1.0",
 ]
@@ -105,6 +141,7 @@ name = "annotated-types"
 version = "0.7.0"
 requires_python = ">=3.8"
 summary = "Reusable constraint types to use with typing.Annotated"
+groups = ["default"]
 dependencies = [
     "typing-extensions>=4.0.0; python_version < \"3.9\"",
 ]
@@ -113,19 +150,12 @@ files = [
     {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
 ]
 
-[[package]]
-name = "asciitree"
-version = "0.3.3"
-summary = "Draws ASCII trees."
-files = [
-    {file = "asciitree-0.3.3.tar.gz", hash = "sha256:4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e"},
-]
-
 [[package]]
 name = "attrs"
 version = "23.2.0"
 requires_python = ">=3.7"
 summary = "Classes Without Boilerplate"
+groups = ["default"]
 dependencies = [
     "importlib-metadata; python_version < \"3.8\"",
 ]
@@ -136,32 +166,28 @@ files = [
 
 [[package]]
 name = "bioio"
-version = "1.1.0"
-requires_python = ">=3.9"
+version = "3.0.0"
+requires_python = ">=3.10"
 summary = "Image reading, metadata management, and image writing for Microscopy images in Python"
+groups = ["default"]
 dependencies = [
-    "bioio-base>=0.9.1",
+    "bioio-base==3.0.0",
     "dask[array]>=2021.4.1",
-    "fsspec>=2022.8.0",
-    "imageio[ffmpeg]<2.28.0,>=2.11.0",
-    "ngff-zarr>=0.8.2",
-    "numpy<2.0.0,>=1.21.0",
+    "numpy>=1.21.0",
     "ome-types[lxml]>=0.4.0",
-    "ome-zarr>=0.6.1",
     "semver>=3.0.1",
-    "tifffile>=2021.8.30",
-    "zarr<2.18.0,>=2.6.0",
 ]
 files = [
-    {file = "bioio-1.1.0-py3-none-any.whl", hash = "sha256:175eb3466eb3d56fe5673118548e5844fcff5e27f0f14463adfb1a118a3a8d7c"},
-    {file = "bioio-1.1.0.tar.gz", hash = "sha256:a7e22bfa5ec60385057f3e1800b5292e5764ca6bd795e09954315b27bf0d1d3b"},
+    {file = "bioio-3.0.0-py3-none-any.whl", hash = "sha256:c8a796d2ddf0b60fb240603c51c6b7e48fa1b3d8d2da9ade137f67d04f0707c0"},
+    {file = "bioio-3.0.0.tar.gz", hash = "sha256:8be25df70b611e62d1f1c3b11b47e039f3626e08e17e0dc792d824be3e4aeb89"},
 ]
 
 [[package]]
 name = "bioio-base"
-version = "1.0.4"
-requires_python = ">=3.9"
+version = "3.0.0"
+requires_python = ">=3.10"
 summary = "Typing, base classes, and more for BioIO projects."
+groups = ["default"]
 dependencies = [
     "dask[array,distributed]!=2022.5.1,>=2021.4.1",
     "fsspec!=2022.7.0,>=2021.4.0",
@@ -170,70 +196,76 @@ dependencies = [
     "xarray>=2022.6.0",
 ]
 files = [
-    {file = "bioio_base-1.0.4-py3-none-any.whl", hash = "sha256:187ae976323b15250c978527fe271e1a9707f5712f3517ddeff1e160b2515e53"},
-    {file = "bioio_base-1.0.4.tar.gz", hash = "sha256:92fc4f5676e83103333da1903aa3ccc7825a333229b72bfcd200dd3dfdde360b"},
+    {file = "bioio_base-3.0.0-py3-none-any.whl", hash = "sha256:278f44aa79bbd50217521d8a4347716d5b07123f892ba7b7d1a6709c86021724"},
+    {file = "bioio_base-3.0.0.tar.gz", hash = "sha256:47ba5aa50b9c068116b0b505f8c5816c346fc7ad1c65116052c6a734e662d680"},
 ]
 
 [[package]]
 name = "bioio-ome-tiff"
-version = "1.0.0"
-requires_python = ">=3.9"
+version = "1.4.0"
+requires_python = ">=3.10"
 summary = "A BioIO reader plugin for reading tiff files in the OME format."
+groups = ["default"]
 dependencies = [
     "PyYAML>=6.0",
-    "bioio-base>=0.3.0",
+    "bioio-base>=1.4.0",
     "dask[array]>=2021.4.1",
     "fsspec>=2022.8.0",
     "imagecodecs>=2020.5.30",
     "numpy>=1.21",
     "ome-types[lxml]>=0.4.0",
     "pydantic>=1.10.0",
-    "tifffile>=2022.4.22",
+    "tifffile[zarr]<2025.1.10,>=2022.4.22; python_version < \"3.11\"",
+    "tifffile[zarr]>=2025.5.21; python_version >= \"3.11\"",
     "xarray>=0.16.1",
     "xmlschema",
-    "zarr>=2.6",
 ]
 files = [
-    {file = "bioio-ome-tiff-1.0.0.tar.gz", hash = "sha256:05b904cdcd1985d27ab2e36b704d0003d251ef313f22c74831a90306d7755a0f"},
-    {file = "bioio_ome_tiff-1.0.0-py3-none-any.whl", hash = "sha256:50aa7a39161e769c1e21e8f00b32bc562a35167da9470676ab711aa88603d0e9"},
+    {file = "bioio_ome_tiff-1.4.0-py3-none-any.whl", hash = "sha256:98107a847244a7b515c7a8c39b5119e67f4047b63661238b49b3d0cc36a86cd9"},
+    {file = "bioio_ome_tiff-1.4.0.tar.gz", hash = "sha256:0073ff612926ea17c72a32f378d62361e282dd7afbc561e8c0a53316fd8d2e29"},
 ]
 
 [[package]]
 name = "bioio-ome-zarr"
-version = "1.0.1"
-requires_python = ">=3.9"
+version = "3.0.3"
+requires_python = ">=3.11"
 summary = "A BioIO reader plugin for reading Zarr files in the OME format."
+groups = ["default"]
 dependencies = [
-    "bioio-base>=1.0.0",
-    "fsspec>=2022.8.0",
-    "ome-zarr>=0.8.0",
+    "bioio-base>=1.4.0",
+    "fsspec[http]>=2022.8.0",
+    "s3fs>=2023.9.0",
+    "scikit-image!=0.23.0",
     "xarray>=0.16.1",
+    "zarr>=3.1.0",
 ]
 files = [
-    {file = "bioio_ome_zarr-1.0.1-py3-none-any.whl", hash = "sha256:3f51861e86a74c83700702cb1c0ddf5fa9f2c11ad07bc5c07c188d67d2d10b21"},
-    {file = "bioio_ome_zarr-1.0.1.tar.gz", hash = "sha256:8c25f47024d637e1b58b25b71df1ec016703779dcfe1e13da762571f0000762a"},
+    {file = "bioio_ome_zarr-3.0.3-py3-none-any.whl", hash = "sha256:26a2953e365f22583c70309e34b100bc91289b145094ee56c00d1c1aef956fcf"},
+    {file = "bioio_ome_zarr-3.0.3.tar.gz", hash = "sha256:c6b53aff2dde4d5f69222300d39fd9c161a05f5da8641f160e61fe4b4182b7ee"},
 ]
 
 [[package]]
 name = "boto3"
-version = "1.35.12"
-requires_python = ">=3.8"
+version = "1.40.61"
+requires_python = ">=3.9"
 summary = "The AWS SDK for Python"
+groups = ["default"]
 dependencies = [
-    "botocore<1.36.0,>=1.35.12",
+    "botocore<1.41.0,>=1.40.61",
     "jmespath<2.0.0,>=0.7.1",
-    "s3transfer<0.11.0,>=0.10.0",
+    "s3transfer<0.15.0,>=0.14.0",
 ]
 files = [
-    {file = "boto3-1.35.12-py3-none-any.whl", hash = "sha256:acaa7c75cbf483605e3c46e9ac03043a4cf5e9866940122d68b06d1defe00774"},
-    {file = "boto3-1.35.12.tar.gz", hash = "sha256:b32faab174f6f9b75fada27bcf054ab3e8846bd410ed9817d0b511109326b6b1"},
+    {file = "boto3-1.40.61-py3-none-any.whl", hash = "sha256:6b9c57b2a922b5d8c17766e29ed792586a818098efe84def27c8f582b33f898c"},
+    {file = "boto3-1.40.61.tar.gz", hash = "sha256:d6c56277251adf6c2bdd25249feae625abe4966831676689ff23b4694dea5b12"},
 ]
 
 [[package]]
 name = "botocore"
-version = "1.35.12"
-requires_python = ">=3.8"
+version = "1.40.61"
+requires_python = ">=3.9"
 summary = "Low-level, data-driven core of boto 3."
+groups = ["default"]
 dependencies = [
     "jmespath<2.0.0,>=0.7.1",
     "python-dateutil<3.0.0,>=2.1",
@@ -241,8 +273,8 @@ dependencies = [
     "urllib3<1.27,>=1.25.4; python_version < \"3.10\"",
 ]
 files = [
-    {file = "botocore-1.35.12-py3-none-any.whl", hash = "sha256:cb787030415438ea6ff8381f8acd8b1107593d5ebea457fd843a5e36ba19e9a4"},
-    {file = "botocore-1.35.12.tar.gz", hash = "sha256:a8f8230032d090225a93763675a73c208d121bb63ed99f41ee6ad3d51b74b80d"},
+    {file = "botocore-1.40.61-py3-none-any.whl", hash = "sha256:17ebae412692fd4824f99cde0f08d50126dc97954008e5ba2b522eb049238aa7"},
+    {file = "botocore-1.40.61.tar.gz", hash = "sha256:a2487ad69b090f9cccd64cf07c7021cd80ee9c0655ad974f87045b02f3ef52cd"},
 ]
 
 [[package]]
@@ -250,16 +282,34 @@ name = "certifi"
 version = "2024.7.4"
 requires_python = ">=3.6"
 summary = "Python package for providing Mozilla's CA Bundle."
+groups = ["default"]
 files = [
     {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
     {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
 ]
 
+[[package]]
+name = "cgal"
+version = "6.0.1.post202410241521"
+requires_python = ">=3.6"
+summary = "CGAL bindings, allowing to use some of the CGAL library in Python."
+groups = ["default"]
+dependencies = [
+    "numpy",
+]
+files = [
+    {file = "cgal-6.0.1.post202410241521-cp311-cp311-macosx_10_13_x86_64.whl", hash = "sha256:71519601772dcc642247ddc721764f0154badab0e819b09462b3a1e01eb464a7"},
+    {file = "cgal-6.0.1.post202410241521-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:151156aabdb6c95e962d7b1017157faf606e301882278e726a620a7095342b48"},
+    {file = "cgal-6.0.1.post202410241521-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1ebe41ebd1b427f7d7baabbb88f081b40c7b151c1093c3b2699590b7d3a21b52"},
+    {file = "cgal-6.0.1.post202410241521-cp311-cp311-win_amd64.whl", hash = "sha256:7a7eb61238be20f6bee11e13dfcba0e7dbbdceb8b87b125b3497f5303de1e058"},
+]
+
 [[package]]
 name = "charset-normalizer"
 version = "3.3.2"
 requires_python = ">=3.7.0"
 summary = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+groups = ["default"]
 files = [
     {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
     {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
@@ -330,6 +380,7 @@ name = "click"
 version = "8.1.7"
 requires_python = ">=3.7"
 summary = "Composable command line interface toolkit"
+groups = ["default"]
 dependencies = [
     "colorama; platform_system == \"Windows\"",
     "importlib-metadata; python_version < \"3.8\"",
@@ -344,6 +395,7 @@ name = "cloudpickle"
 version = "3.0.0"
 requires_python = ">=3.8"
 summary = "Pickler class to extend the standard pickle.Pickler functionality"
+groups = ["default"]
 files = [
     {file = "cloudpickle-3.0.0-py3-none-any.whl", hash = "sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7"},
     {file = "cloudpickle-3.0.0.tar.gz", hash = "sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882"},
@@ -354,6 +406,8 @@ name = "colorama"
 version = "0.4.6"
 requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 summary = "Cross-platform colored terminal text."
+groups = ["default"]
+marker = "platform_system == \"Windows\""
 files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
@@ -364,6 +418,7 @@ name = "contourpy"
 version = "1.2.1"
 requires_python = ">=3.9"
 summary = "Python library for calculating contours of 2D quadrilateral grids"
+groups = ["default"]
 dependencies = [
     "numpy>=1.20",
 ]
@@ -401,11 +456,36 @@ files = [
     {file = "contourpy-1.2.1.tar.gz", hash = "sha256:4d8908b3bee1c889e547867ca4cdc54e5ab6be6d3e078556814a22457f49423c"},
 ]
 
+[[package]]
+name = "crc32c"
+version = "2.8"
+requires_python = ">=3.7"
+summary = "A python package implementing the crc32c algorithm in hardware and software"
+groups = ["default"]
+files = [
+    {file = "crc32c-2.8-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:e560a97fbb96c9897cb1d9b5076ef12fc12e2e25622530a1afd0de4240f17e1f"},
+    {file = "crc32c-2.8-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6762d276d90331a490ef7e71ffee53b9c0eb053bd75a272d786f3b08d3fe3671"},
+    {file = "crc32c-2.8-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:60670569f5ede91e39f48fb0cb4060e05b8d8704dd9e17ede930bf441b2f73ef"},
+    {file = "crc32c-2.8-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl", hash = "sha256:711743da6ccc70b3c6718c328947b0b6f34a1fe6a6c27cc6c1d69cc226bf70e9"},
+    {file = "crc32c-2.8-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:5eb4094a2054774f13b26f21bf56792bb44fa1fcee6c6ad099387a43ffbfb4fa"},
+    {file = "crc32c-2.8-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:fff15bf2bd3e95780516baae935ed12be88deaa5ebe6143c53eb0d26a7bdc7b7"},
+    {file = "crc32c-2.8-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:4c0e11e3826668121fa53e0745635baf5e4f0ded437e8ff63ea56f38fc4f970a"},
+    {file = "crc32c-2.8-cp311-cp311-win32.whl", hash = "sha256:38f915336715d1f1353ab07d7d786f8a789b119e273aea106ba55355dfc9101d"},
+    {file = "crc32c-2.8-cp311-cp311-win_amd64.whl", hash = "sha256:60e0a765b1caab8d31b2ea80840639253906a9351d4b861551c8c8625ea20f86"},
+    {file = "crc32c-2.8-pp311-pypy311_pp73-macosx_10_15_x86_64.whl", hash = "sha256:5833f4071da7ea182c514ba17d1eee8aec3c5be927d798222fbfbbd0f5eea02c"},
+    {file = "crc32c-2.8-pp311-pypy311_pp73-macosx_11_0_arm64.whl", hash = "sha256:1dc4da036126ac07b39dd9d03e93e585ec615a2ad28ff12757aef7de175295a8"},
+    {file = "crc32c-2.8-pp311-pypy311_pp73-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl", hash = "sha256:15905fa78344654e241371c47e6ed2411f9eeb2b8095311c68c88eccf541e8b4"},
+    {file = "crc32c-2.8-pp311-pypy311_pp73-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:c596f918688821f796434e89b431b1698396c38bf0b56de873621528fe3ecb1e"},
+    {file = "crc32c-2.8-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:8d23c4fe01b3844cb6e091044bc1cebdef7d16472e058ce12d9fadf10d2614af"},
+    {file = "crc32c-2.8.tar.gz", hash = "sha256:578728964e59c47c356aeeedee6220e021e124b9d3e8631d95d9a5e5f06e261c"},
+]
+
 [[package]]
 name = "cycler"
 version = "0.12.1"
 requires_python = ">=3.8"
 summary = "Composable style cycles"
+groups = ["default"]
 files = [
     {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
     {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
@@ -416,6 +496,7 @@ name = "dask"
 version = "2024.7.0"
 requires_python = ">=3.9"
 summary = "Parallel PyData with Task Scheduling"
+groups = ["default"]
 dependencies = [
     "click>=8.1",
     "cloudpickle>=1.5.0",
@@ -437,6 +518,7 @@ version = "2024.7.0"
 extras = ["array", "distributed"]
 requires_python = ">=3.9"
 summary = "Parallel PyData with Task Scheduling"
+groups = ["default"]
 dependencies = [
     "dask==2024.7.0",
     "distributed==2024.7.0",
@@ -453,6 +535,7 @@ version = "2024.7.0"
 extras = ["array"]
 requires_python = ">=3.9"
 summary = "Parallel PyData with Task Scheduling"
+groups = ["default"]
 dependencies = [
     "dask==2024.7.0",
     "numpy>=1.21",
@@ -467,6 +550,7 @@ name = "distributed"
 version = "2024.7.0"
 requires_python = ">=3.9"
 summary = "Distributed scheduler for Dask"
+groups = ["default"]
 dependencies = [
     "click>=8.0",
     "cloudpickle>=1.5.0",
@@ -489,31 +573,37 @@ files = [
     {file = "distributed-2024.7.0.tar.gz", hash = "sha256:c8a1a71e14e73b340abee443ece5c8119465f97bdb8a00ff6933b945840a0052"},
 ]
 
+[[package]]
+name = "donfig"
+version = "0.8.1.post1"
+requires_python = ">=3.8"
+summary = "Python package for configuring a python package"
+groups = ["default"]
+dependencies = [
+    "pyyaml",
+]
+files = [
+    {file = "donfig-0.8.1.post1-py3-none-any.whl", hash = "sha256:2a3175ce74a06109ff9307d90a230f81215cbac9a751f4d1c6194644b8204f9d"},
+    {file = "donfig-0.8.1.post1.tar.gz", hash = "sha256:3bef3413a4c1c601b585e8d297256d0c1470ea012afa6e8461dc28bfb7c23f52"},
+]
+
 [[package]]
 name = "elementpath"
 version = "4.4.0"
 requires_python = ">=3.8"
 summary = "XPath 1.0/2.0/3.0/3.1 parsers and selectors for ElementTree and lxml"
+groups = ["default"]
 files = [
     {file = "elementpath-4.4.0-py3-none-any.whl", hash = "sha256:cda092281afe508ece1bf65373905b30196c9426f3730cfea46059e103a131bd"},
     {file = "elementpath-4.4.0.tar.gz", hash = "sha256:dfc4b8ca3d87966dcb0df40b5b6d04a98f053683271930fad9e7fa000924dfb2"},
 ]
 
-[[package]]
-name = "fasteners"
-version = "0.19"
-requires_python = ">=3.6"
-summary = "A python package that provides useful locks"
-files = [
-    {file = "fasteners-0.19-py3-none-any.whl", hash = "sha256:758819cb5d94cdedf4e836988b74de396ceacb8e2794d21f82d131fd9ee77237"},
-    {file = "fasteners-0.19.tar.gz", hash = "sha256:b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c"},
-]
-
 [[package]]
 name = "fonttools"
 version = "4.53.1"
 requires_python = ">=3.8"
 summary = "Tools to manipulate font files"
+groups = ["default"]
 files = [
     {file = "fonttools-4.53.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:0679a30b59d74b6242909945429dbddb08496935b82f91ea9bf6ad240ec23397"},
     {file = "fonttools-4.53.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e8bf06b94694251861ba7fdeea15c8ec0967f84c3d4143ae9daf42bbc7717fe3"},
@@ -548,6 +638,7 @@ name = "frozenlist"
 version = "1.4.1"
 requires_python = ">=3.8"
 summary = "A list-like structure which implements collections.abc.MutableSequence"
+groups = ["default"]
 files = [
     {file = "frozenlist-1.4.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f9aa1878d1083b276b0196f2dfbe00c9b7e752475ed3b682025ff20c1c1f51ac"},
     {file = "frozenlist-1.4.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:29acab3f66f0f24674b7dc4736477bcd4bc3ad4b896f5f45379a67bce8b96868"},
@@ -615,27 +706,29 @@ files = [
 
 [[package]]
 name = "fsspec"
-version = "2023.6.0"
-requires_python = ">=3.8"
+version = "2025.10.0"
+requires_python = ">=3.9"
 summary = "File-system specification"
+groups = ["default"]
 files = [
-    {file = "fsspec-2023.6.0-py3-none-any.whl", hash = "sha256:1cbad1faef3e391fba6dc005ae9b5bdcbf43005c9167ce78c915549c352c869a"},
-    {file = "fsspec-2023.6.0.tar.gz", hash = "sha256:d0b2f935446169753e7a5c5c55681c54ea91996cc67be93c39a154fb3a2742af"},
+    {file = "fsspec-2025.10.0-py3-none-any.whl", hash = "sha256:7c7712353ae7d875407f97715f0e1ffcc21e33d5b24556cb1e090ae9409ec61d"},
+    {file = "fsspec-2025.10.0.tar.gz", hash = "sha256:b6789427626f068f9a83ca4e8a3cc050850b6c0f71f99ddb4f542b8266a26a59"},
 ]
 
 [[package]]
 name = "fsspec"
-version = "2023.6.0"
-extras = ["s3"]
-requires_python = ">=3.8"
+version = "2025.10.0"
+extras = ["http"]
+requires_python = ">=3.9"
 summary = "File-system specification"
+groups = ["default"]
 dependencies = [
-    "fsspec==2023.6.0",
-    "s3fs",
+    "aiohttp!=4.0.0a0,!=4.0.0a1",
+    "fsspec==2025.10.0",
 ]
 files = [
-    {file = "fsspec-2023.6.0-py3-none-any.whl", hash = "sha256:1cbad1faef3e391fba6dc005ae9b5bdcbf43005c9167ce78c915549c352c869a"},
-    {file = "fsspec-2023.6.0.tar.gz", hash = "sha256:d0b2f935446169753e7a5c5c55681c54ea91996cc67be93c39a154fb3a2742af"},
+    {file = "fsspec-2025.10.0-py3-none-any.whl", hash = "sha256:7c7712353ae7d875407f97715f0e1ffcc21e33d5b24556cb1e090ae9409ec61d"},
+    {file = "fsspec-2025.10.0.tar.gz", hash = "sha256:b6789427626f068f9a83ca4e8a3cc050850b6c0f71f99ddb4f542b8266a26a59"},
 ]
 
 [[package]]
@@ -643,6 +736,7 @@ name = "idna"
 version = "3.7"
 requires_python = ">=3.5"
 summary = "Internationalized Domain Names in Applications (IDNA)"
+groups = ["default"]
 files = [
     {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
     {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
@@ -653,6 +747,7 @@ name = "imagecodecs"
 version = "2024.6.1"
 requires_python = ">=3.9"
 summary = "Image transformation, compression, and decompression codecs"
+groups = ["default"]
 dependencies = [
     "numpy",
 ]
@@ -692,6 +787,7 @@ name = "imageio"
 version = "2.27.0"
 requires_python = ">=3.7"
 summary = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
+groups = ["default"]
 dependencies = [
     "numpy",
     "pillow>=8.3.2",
@@ -701,44 +797,13 @@ files = [
     {file = "imageio-2.27.0.tar.gz", hash = "sha256:ee269c957785ef0373cc7a7323185956d83ec05e6cdf20b42a03ba7b74ac58c6"},
 ]
 
-[[package]]
-name = "imageio-ffmpeg"
-version = "0.5.1"
-requires_python = ">=3.5"
-summary = "FFMPEG wrapper for Python"
-dependencies = [
-    "setuptools",
-]
-files = [
-    {file = "imageio-ffmpeg-0.5.1.tar.gz", hash = "sha256:0ed7a9b31f560b0c9d929c5291cd430edeb9bed3ce9a497480e536dd4326484c"},
-    {file = "imageio_ffmpeg-0.5.1-py3-none-macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl", hash = "sha256:1460e84712b9d06910c1f7bb524096b0341d4b7844cea6c20e099d0a24e795b1"},
-    {file = "imageio_ffmpeg-0.5.1-py3-none-manylinux2010_x86_64.whl", hash = "sha256:5289f75c7f755b499653f3209fea4efd1430cba0e39831c381aad2d458f7a316"},
-    {file = "imageio_ffmpeg-0.5.1-py3-none-manylinux2014_aarch64.whl", hash = "sha256:7fa9132a291d5eb28c44553550deb40cbdab831f2a614e55360301a6582eb205"},
-    {file = "imageio_ffmpeg-0.5.1-py3-none-win32.whl", hash = "sha256:89efe2c79979d8174ba8476deb7f74d74c331caee3fb2b65ba2883bec0737625"},
-    {file = "imageio_ffmpeg-0.5.1-py3-none-win_amd64.whl", hash = "sha256:1521e79e253bedbdd36a547e0cbd94a025ba0b558e17f08fea687d805a0e4698"},
-]
-
-[[package]]
-name = "imageio"
-version = "2.27.0"
-extras = ["ffmpeg"]
-requires_python = ">=3.7"
-summary = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
-dependencies = [
-    "imageio-ffmpeg",
-    "imageio==2.27.0",
-    "psutil",
-]
-files = [
-    {file = "imageio-2.27.0-py3-none-any.whl", hash = "sha256:24c6ad7d000e64eacc2861c402b6fb128f370cb0a6623cf796d83bca0d0d14d3"},
-    {file = "imageio-2.27.0.tar.gz", hash = "sha256:ee269c957785ef0373cc7a7323185956d83ec05e6cdf20b42a03ba7b74ac58c6"},
-]
-
 [[package]]
 name = "importlib-metadata"
 version = "8.0.0"
 requires_python = ">=3.8"
 summary = "Read metadata from Python packages"
+groups = ["default"]
+marker = "python_version < \"3.12\""
 dependencies = [
     "typing-extensions>=3.6.4; python_version < \"3.8\"",
     "zipp>=0.5",
@@ -748,83 +813,12 @@ files = [
     {file = "importlib_metadata-8.0.0.tar.gz", hash = "sha256:188bd24e4c346d3f0a933f275c2fec67050326a856b9a359881d7c2a697e8812"},
 ]
 
-[[package]]
-name = "importlib-resources"
-version = "6.4.4"
-requires_python = ">=3.8"
-summary = "Read resources from Python packages"
-dependencies = [
-    "zipp>=3.1.0; python_version < \"3.10\"",
-]
-files = [
-    {file = "importlib_resources-6.4.4-py3-none-any.whl", hash = "sha256:dda242603d1c9cd836c3368b1174ed74cb4049ecd209e7a1a0104620c18c5c11"},
-    {file = "importlib_resources-6.4.4.tar.gz", hash = "sha256:20600c8b7361938dc0bb2d5ec0297802e575df486f5a544fa414da65e13721f7"},
-]
-
-[[package]]
-name = "itkwasm"
-version = "1.0b178"
-requires_python = ">=3.8"
-summary = "Python interface to itk-wasm WebAssembly (Wasm) modules."
-dependencies = [
-    "importlib-metadata; python_version < \"3.10\"",
-    "numpy",
-    "platformdirs; sys_platform != \"emscripten\"",
-    "typing-extensions",
-    "wasmtime>=13.0.2; sys_platform != \"emscripten\"",
-]
-files = [
-    {file = "itkwasm-1.0b178-py3-none-any.whl", hash = "sha256:c6e77b76492ef5d6d20fc822934aee230a438ab752b8ebc93fd63944e7832915"},
-    {file = "itkwasm-1.0b178.tar.gz", hash = "sha256:3fa34b9c60ebd234a12cdbeeab0ce5e3e06334da5d8600eba365aa13d9896ded"},
-]
-
-[[package]]
-name = "itkwasm-downsample"
-version = "1.4.0"
-requires_python = ">=3.8"
-summary = "Pipelines for downsampling images."
-dependencies = [
-    "itkwasm-downsample-emscripten; sys_platform == \"emscripten\"",
-    "itkwasm-downsample-wasi; sys_platform != \"emscripten\"",
-    "itkwasm>=1.0.b145",
-]
-files = [
-    {file = "itkwasm_downsample-1.4.0-py3-none-any.whl", hash = "sha256:728898246e41e036ba5f7773ce37456bfa184b6a957e729dcf227d5c0fdd230b"},
-    {file = "itkwasm_downsample-1.4.0.tar.gz", hash = "sha256:c30cc4a7df33e2b6c6ffa793e8df8235a450cac34de4662312e29e7b04abc2d8"},
-]
-
-[[package]]
-name = "itkwasm-downsample-emscripten"
-version = "1.4.0"
-requires_python = ">=3.8"
-summary = "Pipelines for downsampling images."
-dependencies = [
-    "itkwasm>=1.0.b145",
-]
-files = [
-    {file = "itkwasm_downsample_emscripten-1.4.0-py3-none-any.whl", hash = "sha256:1ba3dfcf5db256ca2e78853bd314ddcd38d18428e5d0e23cabb0c3c3c4853281"},
-    {file = "itkwasm_downsample_emscripten-1.4.0.tar.gz", hash = "sha256:99696918c6afb301d55ea03264880c6a144fa22dce2104f1ac0c7d2f413662bc"},
-]
-
-[[package]]
-name = "itkwasm-downsample-wasi"
-version = "1.4.0"
-requires_python = ">=3.8"
-summary = "Pipelines for downsampling images."
-dependencies = [
-    "importlib-resources",
-    "itkwasm>=1.0.b145",
-]
-files = [
-    {file = "itkwasm_downsample_wasi-1.4.0-py3-none-any.whl", hash = "sha256:167a7b79d77d01db07cf0fd263cdbc24fac860a57dbc01e89db070e2b10c8f2b"},
-    {file = "itkwasm_downsample_wasi-1.4.0.tar.gz", hash = "sha256:8927127c65294fa1c08550987ad4a50019c31629101f50af0567fa02aae8cee8"},
-]
-
 [[package]]
 name = "jinja2"
 version = "3.1.4"
 requires_python = ">=3.7"
 summary = "A very fast and expressive template engine."
+groups = ["default"]
 dependencies = [
     "MarkupSafe>=2.0",
 ]
@@ -838,6 +832,7 @@ name = "jmespath"
 version = "1.0.1"
 requires_python = ">=3.7"
 summary = "JSON Matching Expressions"
+groups = ["default"]
 files = [
     {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"},
     {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"},
@@ -847,6 +842,7 @@ files = [
 name = "jsonlines"
 version = "1.2.0"
 summary = "Library with helpers for the jsonlines file format"
+groups = ["default"]
 dependencies = [
     "six",
 ]
@@ -860,6 +856,7 @@ name = "jsonschema"
 version = "4.23.0"
 requires_python = ">=3.8"
 summary = "An implementation of JSON Schema validation for Python"
+groups = ["default"]
 dependencies = [
     "attrs>=22.2.0",
     "importlib-resources>=1.4.0; python_version < \"3.9\"",
@@ -878,6 +875,7 @@ name = "jsonschema-specifications"
 version = "2023.12.1"
 requires_python = ">=3.8"
 summary = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+groups = ["default"]
 dependencies = [
     "importlib-resources>=1.4.0; python_version < \"3.9\"",
     "referencing>=0.31.0",
@@ -891,6 +889,7 @@ files = [
 name = "kaleido"
 version = "0.2.1"
 summary = "Static image export for web-based visualization libraries with zero dependencies"
+groups = ["default"]
 dependencies = [
     "pathlib; python_version < \"3.4\"",
 ]
@@ -903,11 +902,31 @@ files = [
     {file = "kaleido-0.2.1-py2.py3-none-win_amd64.whl", hash = "sha256:4670985f28913c2d063c5734d125ecc28e40810141bdb0a46f15b76c1d45f23c"},
 ]
 
+[[package]]
+name = "kerchunk"
+version = "0.2.9"
+requires_python = ">=3.11"
+summary = "Functions to make reference descriptions for ReferenceFileSystem"
+groups = ["default"]
+marker = "python_version >= \"3.11\""
+dependencies = [
+    "fsspec>=2025.2.0",
+    "numcodecs",
+    "numpy",
+    "ujson",
+    "zarr>=3.0.1",
+]
+files = [
+    {file = "kerchunk-0.2.9-py3-none-any.whl", hash = "sha256:5f7ff385ace07c62bd0ae5db639cac8b441169fea2389bb006fd209549f699c2"},
+    {file = "kerchunk-0.2.9.tar.gz", hash = "sha256:86a54da9a57a94fd6fb97be786e2d83182d3d8e4fd7c0ea2b67cde3d0641df7d"},
+]
+
 [[package]]
 name = "kiwisolver"
 version = "1.4.5"
 requires_python = ">=3.7"
 summary = "A fast implementation of the Cassowary constraint solver"
+groups = ["default"]
 dependencies = [
     "typing-extensions; python_version < \"3.8\"",
 ]
@@ -965,6 +984,7 @@ name = "lazy-loader"
 version = "0.4"
 requires_python = ">=3.7"
 summary = "Makes it easy to load subpackages and functions on demand."
+groups = ["default"]
 dependencies = [
     "importlib-metadata; python_version < \"3.8\"",
     "packaging",
@@ -979,6 +999,7 @@ name = "locket"
 version = "1.0.0"
 requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 summary = "File-based locks for Python on Linux and Windows"
+groups = ["default"]
 files = [
     {file = "locket-1.0.0-py2.py3-none-any.whl", hash = "sha256:b6c819a722f7b6bd955b80781788e4a66a55628b858d347536b7e81325a3a5e3"},
     {file = "locket-1.0.0.tar.gz", hash = "sha256:5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632"},
@@ -989,6 +1010,7 @@ name = "lxml"
 version = "4.9.4"
 requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
 summary = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
+groups = ["default"]
 files = [
     {file = "lxml-4.9.4-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:056a17eaaf3da87a05523472ae84246f87ac2f29a53306466c22e60282e54ff8"},
     {file = "lxml-4.9.4-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_24_i686.whl", hash = "sha256:aaa5c173a26960fe67daa69aa93d6d6a1cd714a6eb13802d4e4bd1d24a530644"},
@@ -1046,24 +1068,12 @@ files = [
     {file = "lxml-4.9.4.tar.gz", hash = "sha256:b1541e50b78e15fa06a2670157a1962ef06591d4c998b998047fff5e3236880e"},
 ]
 
-[[package]]
-name = "markdown-it-py"
-version = "3.0.0"
-requires_python = ">=3.8"
-summary = "Python port of markdown-it. Markdown parsing, done right!"
-dependencies = [
-    "mdurl~=0.1",
-]
-files = [
-    {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"},
-    {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"},
-]
-
 [[package]]
 name = "markupsafe"
 version = "2.1.5"
 requires_python = ">=3.7"
 summary = "Safely add untrusted strings to HTML/XML markup."
+groups = ["default"]
 files = [
     {file = "MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a17a92de5231666cfbe003f0e4b9b3a7ae3afb1ec2845aadc2bacc93ff85febc"},
     {file = "MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:72b6be590cc35924b02c78ef34b467da4ba07e4e0f0454a2c5907f473fc50ce5"},
@@ -1113,6 +1123,7 @@ name = "matplotlib"
 version = "3.9.1"
 requires_python = ">=3.9"
 summary = "Python plotting package"
+groups = ["default"]
 dependencies = [
     "contourpy>=1.0.1",
     "cycler>=0.10",
@@ -1147,21 +1158,12 @@ files = [
     {file = "matplotlib-3.9.1.tar.gz", hash = "sha256:de06b19b8db95dd33d0dc17c926c7c9ebed9f572074b6fac4f65068a6814d010"},
 ]
 
-[[package]]
-name = "mdurl"
-version = "0.1.2"
-requires_python = ">=3.7"
-summary = "Markdown URL utilities"
-files = [
-    {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"},
-    {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
-]
-
 [[package]]
 name = "msgpack"
 version = "1.0.8"
 requires_python = ">=3.8"
 summary = "MessagePack serializer"
+groups = ["default"]
 files = [
     {file = "msgpack-1.0.8-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:505fe3d03856ac7d215dbe005414bc28505d26f0c128906037e66d98c4e95868"},
     {file = "msgpack-1.0.8-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e6b7842518a63a9f17107eb176320960ec095a8ee3b4420b5f688e24bf50c53c"},
@@ -1215,6 +1217,7 @@ name = "multidict"
 version = "6.0.5"
 requires_python = ">=3.7"
 summary = "multidict implementation"
+groups = ["default"]
 files = [
     {file = "multidict-6.0.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:228b644ae063c10e7f324ab1ab6b548bdf6f8b47f3ec234fef1093bc2735e5f9"},
     {file = "multidict-6.0.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:896ebdcf62683551312c30e20614305f53125750803b614e9e6ce74a96232604"},
@@ -1285,59 +1288,49 @@ name = "networkx"
 version = "3.2.1"
 requires_python = ">=3.9"
 summary = "Python package for creating and manipulating graphs and networks"
+groups = ["default"]
 files = [
     {file = "networkx-3.2.1-py3-none-any.whl", hash = "sha256:f18c69adc97877c42332c170849c96cefa91881c99a7cb3e95b7c659ebdc1ec2"},
     {file = "networkx-3.2.1.tar.gz", hash = "sha256:9f1bb5cf3409bf324e0a722c20bdb4c20ee39bf1c30ce8ae499c8502b0b5e0c6"},
 ]
 
 [[package]]
-name = "ngff-zarr"
-version = "0.8.7"
-requires_python = ">=3.8"
-summary = "A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation."
+name = "numcodecs"
+version = "0.16.3"
+requires_python = ">=3.11"
+summary = "A Python package providing buffer compression and transformation codecs for use in data storage and communication applications."
+groups = ["default"]
 dependencies = [
-    "dask[array]",
-    "itkwasm-downsample>=1.2.0",
-    "itkwasm>=1.0b171",
-    "numpy",
-    "platformdirs",
-    "psutil; sys_platform != \"emscripten\"",
-    "rich",
-    "rich-argparse",
+    "numpy>=1.24",
     "typing-extensions",
-    "zarr",
 ]
 files = [
-    {file = "ngff_zarr-0.8.7-py3-none-any.whl", hash = "sha256:c864f69300bb549a6ddc0092803fc2f69672a5b5d10518bea5d17c5004d1ae69"},
-    {file = "ngff_zarr-0.8.7.tar.gz", hash = "sha256:f29ac42dc7295ab59289560f6d283d56bb075cbf1e783ea0e4b7da542066049b"},
+    {file = "numcodecs-0.16.3-cp311-cp311-macosx_10_13_x86_64.whl", hash = "sha256:95c9f2a49bef10cf91ad614a761cba9bfe96656b60c12540e1080de5d909b4ca"},
+    {file = "numcodecs-0.16.3-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:e2afe73d5ebaf9ca0cd5c83aad945da80d29a33d860a80d43a7248491d8813ff"},
+    {file = "numcodecs-0.16.3-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:913f08194d82dcb37594e6705e6d4ae6ccd4b6571500b832fb3e4a155de1dfe8"},
+    {file = "numcodecs-0.16.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:85a7f1cae9eb18b85709af46570bf9c60056e7155c4c8f610e8080c68124d0e5"},
+    {file = "numcodecs-0.16.3-cp311-cp311-win_amd64.whl", hash = "sha256:f7bb7f2c46eb7ec8a1c5f8d8fe1a72c222256dd6d6df5af9eaac7a6b905f3575"},
+    {file = "numcodecs-0.16.3.tar.gz", hash = "sha256:53d705865faaf0a7927c973af3777532001c8fbb653de119c1e844608614d799"},
 ]
 
 [[package]]
 name = "numcodecs"
-version = "0.12.1"
-requires_python = ">=3.8"
+version = "0.16.3"
+extras = ["crc32c"]
+requires_python = ">=3.11"
 summary = "A Python package providing buffer compression and transformation codecs for use in data storage and communication applications."
+groups = ["default"]
 dependencies = [
-    "numpy>=1.7",
+    "crc32c>=2.7",
+    "numcodecs==0.16.3",
 ]
 files = [
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 ]
 
 [[package]]
@@ -1345,6 +1338,7 @@ name = "numpy"
 version = "1.26.4"
 requires_python = ">=3.9"
 summary = "Fundamental package for array computing in Python"
+groups = ["default"]
 files = [
     {file = "numpy-1.26.4-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:4c66707fabe114439db9068ee468c26bbdf909cac0fb58686a42a24de1760c71"},
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@@ -1370,6 +1364,7 @@ name = "ome-types"
 version = "0.5.1.post1"
 requires_python = ">=3.8"
 summary = "Python dataclasses for the OME data model"
+groups = ["default"]
 dependencies = [
     "pydantic-compat>=0.1.0",
     "pydantic>=1.9.0",
@@ -1386,6 +1381,7 @@ version = "0.5.1.post1"
 extras = ["lxml"]
 requires_python = ">=3.8"
 summary = "Python dataclasses for the OME data model"
+groups = ["default"]
 dependencies = [
     "lxml>=4.8.0",
     "ome-types==0.5.1.post1",
@@ -1395,34 +1391,12 @@ files = [
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 ]
 
-[[package]]
-name = "ome-zarr"
-version = "0.9.0"
-requires_python = ">=3.6"
-summary = "Implementation of images in Zarr files."
-dependencies = [
-    "aiohttp<4",
-    "dask",
-    "dataclasses; python_version < \"3.7\"",
-    "distributed",
-    "fsspec[s3]!=2021.07.0,>=0.8",
-    "numpy",
-    "requests",
-    "scikit-image",
-    "tifffile<2020.09.22; python_version < \"3.7\"",
-    "toolz",
-    "zarr>=2.8.1",
-]
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-
 [[package]]
 name = "packaging"
 version = "24.1"
 requires_python = ">=3.8"
 summary = "Core utilities for Python packages"
+groups = ["default"]
 files = [
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@@ -1433,6 +1407,7 @@ name = "pandas"
 version = "2.2.2"
 requires_python = ">=3.9"
 summary = "Powerful data structures for data analysis, time series, and statistics"
+groups = ["default"]
 dependencies = [
     "numpy>=1.22.4; python_version < \"3.11\"",
     "numpy>=1.23.2; python_version == \"3.11\"",
@@ -1471,6 +1446,7 @@ name = "partd"
 version = "1.4.2"
 requires_python = ">=3.9"
 summary = "Appendable key-value storage"
+groups = ["default"]
 dependencies = [
     "locket",
     "toolz",
@@ -1484,6 +1460,7 @@ files = [
 name = "patsy"
 version = "0.5.6"
 summary = "A Python package for describing statistical models and for building design matrices."
+groups = ["default"]
 dependencies = [
     "numpy>=1.4",
     "six",
@@ -1498,6 +1475,7 @@ name = "pillow"
 version = "10.4.0"
 requires_python = ">=3.8"
 summary = "Python Imaging Library (Fork)"
+groups = ["default"]
 files = [
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@@ -1576,6 +1554,7 @@ name = "platformdirs"
 version = "4.2.2"
 requires_python = ">=3.8"
 summary = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
+groups = ["default"]
 files = [
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@@ -1586,6 +1565,7 @@ name = "plotly"
 version = "5.23.0"
 requires_python = ">=3.8"
 summary = "An open-source, interactive data visualization library for Python"
+groups = ["default"]
 dependencies = [
     "packaging",
     "tenacity>=6.2.0",
@@ -1599,6 +1579,7 @@ files = [
 name = "point-cloud-utils"
 version = "0.30.4"
 summary = "A Python library for common tasks on 3D point clouds and meshes"
+groups = ["default"]
 dependencies = [
     "numpy",
     "scipy",
@@ -1622,6 +1603,7 @@ name = "pooch"
 version = "1.8.2"
 requires_python = ">=3.7"
 summary = "A friend to fetch your data files"
+groups = ["default"]
 dependencies = [
     "packaging>=20.0",
     "platformdirs>=2.5.0",
@@ -1637,6 +1619,7 @@ name = "psutil"
 version = "6.0.0"
 requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 summary = "Cross-platform lib for process and system monitoring in Python."
+groups = ["default"]
 files = [
     {file = "psutil-6.0.0-cp36-abi3-macosx_10_9_x86_64.whl", hash = "sha256:c588a7e9b1173b6e866756dde596fd4cad94f9399daf99ad8c3258b3cb2b47a0"},
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@@ -1653,6 +1636,7 @@ name = "pydantic"
 version = "2.8.2"
 requires_python = ">=3.8"
 summary = "Data validation using Python type hints"
+groups = ["default"]
 dependencies = [
     "annotated-types>=0.4.0",
     "pydantic-core==2.20.1",
@@ -1669,6 +1653,7 @@ name = "pydantic-compat"
 version = "0.1.2"
 requires_python = ">=3.7"
 summary = "Compatibility layer for pydantic v1/v2"
+groups = ["default"]
 dependencies = [
     "importlib-metadata; python_version < \"3.8\"",
     "pydantic",
@@ -1683,6 +1668,7 @@ name = "pydantic-core"
 version = "2.20.1"
 requires_python = ">=3.8"
 summary = "Core functionality for Pydantic validation and serialization"
+groups = ["default"]
 dependencies = [
     "typing-extensions!=4.7.0,>=4.6.0",
 ]
@@ -1766,21 +1752,12 @@ files = [
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 ]
 
-[[package]]
-name = "pygments"
-version = "2.18.0"
-requires_python = ">=3.8"
-summary = "Pygments is a syntax highlighting package written in Python."
-files = [
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-]
-
 [[package]]
 name = "pyparsing"
 version = "3.1.2"
 requires_python = ">=3.6.8"
 summary = "pyparsing module - Classes and methods to define and execute parsing grammars"
+groups = ["default"]
 files = [
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@@ -1791,6 +1768,7 @@ name = "python-dateutil"
 version = "2.8.2"
 requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 summary = "Extensions to the standard Python datetime module"
+groups = ["default"]
 dependencies = [
     "six>=1.5",
 ]
@@ -1803,6 +1781,7 @@ files = [
 name = "pytz"
 version = "2024.1"
 summary = "World timezone definitions, modern and historical"
+groups = ["default"]
 files = [
     {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
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@@ -1813,6 +1792,7 @@ name = "pyvista"
 version = "0.43.10"
 requires_python = ">=3.8"
 summary = "Easier Pythonic interface to VTK"
+groups = ["default"]
 dependencies = [
     "matplotlib>=3.0.1",
     "numpy>=1.21.0",
@@ -1831,6 +1811,7 @@ name = "pyyaml"
 version = "6.0.1"
 requires_python = ">=3.6"
 summary = "YAML parser and emitter for Python"
+groups = ["default"]
 files = [
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@@ -1871,6 +1852,7 @@ name = "quilt3"
 version = "6.0.0"
 requires_python = ">=3.9"
 summary = "Quilt: where data comes together"
+groups = ["default"]
 dependencies = [
     "PyYAML>=5.1",
     "boto3>=1.21.7",
@@ -1893,6 +1875,7 @@ name = "referencing"
 version = "0.35.1"
 requires_python = ">=3.8"
 summary = "JSON Referencing + Python"
+groups = ["default"]
 dependencies = [
     "attrs>=22.2.0",
     "rpds-py>=0.7.0",
@@ -1907,6 +1890,7 @@ name = "requests"
 version = "2.32.3"
 requires_python = ">=3.8"
 summary = "Python HTTP for Humans."
+groups = ["default"]
 dependencies = [
     "certifi>=2017.4.17",
     "charset-normalizer<4,>=2",
@@ -1922,6 +1906,7 @@ files = [
 name = "requests-futures"
 version = "1.0.0"
 summary = "Asynchronous Python HTTP for Humans."
+groups = ["default"]
 dependencies = [
     "futures>=2.1.3; python_version < \"3.2\"",
     "requests>=1.2.0",
@@ -1931,39 +1916,12 @@ files = [
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 ]
 
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-version = "13.8.0"
-requires_python = ">=3.7.0"
-summary = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
-dependencies = [
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-    "pygments<3.0.0,>=2.13.0",
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-version = "1.5.2"
-requires_python = ">=3.8"
-summary = "Rich help formatters for argparse and optparse"
-dependencies = [
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-]
-
 [[package]]
 name = "rpds-py"
 version = "0.20.0"
 requires_python = ">=3.8"
 summary = "Python bindings to Rust's persistent data structures (rpds)"
+groups = ["default"]
 files = [
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@@ -2009,47 +1967,50 @@ files = [
 
 [[package]]
 name = "rtree"
-version = "1.3.0"
-requires_python = ">=3.8"
+version = "1.4.1"
+requires_python = ">=3.9"
 summary = "R-Tree spatial index for Python GIS"
+groups = ["default"]
 files = [
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 [[package]]
 name = "s3fs"
-version = "0.4.2"
-requires_python = ">= 3.5"
+version = "2025.10.0"
+requires_python = ">=3.9"
 summary = "Convenient Filesystem interface over S3"
+groups = ["default"]
 dependencies = [
-    "botocore>=1.12.91",
-    "fsspec>=0.6.0",
+    "aiobotocore<3.0.0,>=2.5.4",
+    "aiohttp!=4.0.0a0,!=4.0.0a1",
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+    {file = "s3fs-2025.10.0-py3-none-any.whl", hash = "sha256:da7ef25efc1541f5fca8e1116361e49ea1081f83f4e8001fbd77347c625da28a"},
+    {file = "s3fs-2025.10.0.tar.gz", hash = "sha256:e8be6cddc77aceea1681ece0f472c3a7f8ef71a0d2acddb1cc92bb6afa3e9e4f"},
 ]
 
 [[package]]
 name = "s3transfer"
-version = "0.10.2"
-requires_python = ">=3.8"
+version = "0.14.0"
+requires_python = ">=3.9"
 summary = "An Amazon S3 Transfer Manager"
+groups = ["default"]
 dependencies = [
-    "botocore<2.0a.0,>=1.33.2",
+    "botocore<2.0a.0,>=1.37.4",
 ]
 files = [
-    {file = "s3transfer-0.10.2-py3-none-any.whl", hash = "sha256:eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69"},
-    {file = "s3transfer-0.10.2.tar.gz", hash = "sha256:0711534e9356d3cc692fdde846b4a1e4b0cb6519971860796e6bc4c7aea00ef6"},
+    {file = "s3transfer-0.14.0-py3-none-any.whl", hash = "sha256:ea3b790c7077558ed1f02a3072fb3cb992bbbd253392f4b6e9e8976941c7d456"},
+    {file = "s3transfer-0.14.0.tar.gz", hash = "sha256:eff12264e7c8b4985074ccce27a3b38a485bb7f7422cc8046fee9be4983e4125"},
 ]
 
 [[package]]
@@ -2057,6 +2018,7 @@ name = "scikit-image"
 version = "0.22.0"
 requires_python = ">=3.9"
 summary = "Image processing in Python"
+groups = ["default"]
 dependencies = [
     "imageio>=2.27",
     "lazy-loader>=0.3",
@@ -2086,6 +2048,7 @@ name = "scikit-posthocs"
 version = "0.9.0"
 requires_python = ">=3.9"
 summary = "Statistical post-hoc analysis and outlier detection algorithms"
+groups = ["default"]
 dependencies = [
     "matplotlib",
     "numpy",
@@ -2104,6 +2067,7 @@ name = "scipy"
 version = "1.14.0"
 requires_python = ">=3.10"
 summary = "Fundamental algorithms for scientific computing in Python"
+groups = ["default"]
 dependencies = [
     "numpy<2.3,>=1.23.5",
 ]
@@ -2140,6 +2104,7 @@ name = "scooby"
 version = "0.10.0"
 requires_python = ">=3.8"
 summary = "A Great Dane turned Python environment detective"
+groups = ["default"]
 files = [
     {file = "scooby-0.10.0-py3-none-any.whl", hash = "sha256:0a3d7e304f8ebb16f69ff7f6360c345d7f50b45f2ddbf7c3d18a6a0dc2cb03a6"},
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@@ -2150,6 +2115,7 @@ name = "seaborn"
 version = "0.13.2"
 requires_python = ">=3.8"
 summary = "Statistical data visualization"
+groups = ["default"]
 dependencies = [
     "matplotlib!=3.6.1,>=3.4",
     "numpy!=1.24.0,>=1.20",
@@ -2165,26 +2131,18 @@ name = "semver"
 version = "3.0.2"
 requires_python = ">=3.7"
 summary = "Python helper for Semantic Versioning (https://semver.org)"
+groups = ["default"]
 files = [
     {file = "semver-3.0.2-py3-none-any.whl", hash = "sha256:b1ea4686fe70b981f85359eda33199d60c53964284e0cfb4977d243e37cf4bf4"},
     {file = "semver-3.0.2.tar.gz", hash = "sha256:6253adb39c70f6e51afed2fa7152bcd414c411286088fb4b9effb133885ab4cc"},
 ]
 
-[[package]]
-name = "setuptools"
-version = "74.0.0"
-requires_python = ">=3.8"
-summary = "Easily download, build, install, upgrade, and uninstall Python packages"
-files = [
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-    {file = "setuptools-74.0.0.tar.gz", hash = "sha256:a85e96b8be2b906f3e3e789adec6a9323abf79758ecfa3065bd740d81158b11e"},
-]
-
 [[package]]
 name = "six"
 version = "1.16.0"
 requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 summary = "Python 2 and 3 compatibility utilities"
+groups = ["default"]
 files = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
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@@ -2194,6 +2152,7 @@ files = [
 name = "sortedcontainers"
 version = "2.4.0"
 summary = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
+groups = ["default"]
 files = [
     {file = "sortedcontainers-2.4.0-py2.py3-none-any.whl", hash = "sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0"},
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@@ -2204,6 +2163,7 @@ name = "statsmodels"
 version = "0.14.2"
 requires_python = ">=3.9"
 summary = "Statistical computations and models for Python"
+groups = ["default"]
 dependencies = [
     "numpy>=1.22.3",
     "packaging>=21.3",
@@ -2232,6 +2192,7 @@ name = "tblib"
 version = "3.0.0"
 requires_python = ">=3.8"
 summary = "Traceback serialization library."
+groups = ["default"]
 files = [
     {file = "tblib-3.0.0-py3-none-any.whl", hash = "sha256:80a6c77e59b55e83911e1e607c649836a69c103963c5f28a46cbeef44acf8129"},
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@@ -2242,6 +2203,7 @@ name = "tenacity"
 version = "8.1.0"
 requires_python = ">=3.6"
 summary = "Retry code until it succeeds"
+groups = ["default"]
 files = [
     {file = "tenacity-8.1.0-py3-none-any.whl", hash = "sha256:35525cd47f82830069f0d6b73f7eb83bc5b73ee2fff0437952cedf98b27653ac"},
     {file = "tenacity-8.1.0.tar.gz", hash = "sha256:e48c437fdf9340f5666b92cd7990e96bc5fc955e1298baf4a907e3972067a445"},
@@ -2249,15 +2211,35 @@ files = [
 
 [[package]]
 name = "tifffile"
-version = "2023.2.28"
-requires_python = ">=3.8"
+version = "2025.10.16"
+requires_python = ">=3.11"
 summary = "Read and write TIFF files"
+groups = ["default"]
 dependencies = [
     "numpy",
 ]
 files = [
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-    {file = "tifffile-2023.2.28.tar.gz", hash = "sha256:2d2baba8dea6609f553fe61853db9a61f715d60ba3bce6a20b5a1ab72407dfed"},
+    {file = "tifffile-2025.10.16-py3-none-any.whl", hash = "sha256:41463d979c1c262b0a5cdef2a7f95f0388a072ad82d899458b154a48609d759c"},
+    {file = "tifffile-2025.10.16.tar.gz", hash = "sha256:425179ec7837ac0e07bc95d2ea5bea9b179ce854967c12ba07fc3f093e58efc1"},
+]
+
+[[package]]
+name = "tifffile"
+version = "2025.10.16"
+extras = ["zarr"]
+requires_python = ">=3.11"
+summary = "Read and write TIFF files"
+groups = ["default"]
+marker = "python_version >= \"3.11\""
+dependencies = [
+    "fsspec",
+    "kerchunk",
+    "tifffile==2025.10.16",
+    "zarr>=3.1.3",
+]
+files = [
+    {file = "tifffile-2025.10.16-py3-none-any.whl", hash = "sha256:41463d979c1c262b0a5cdef2a7f95f0388a072ad82d899458b154a48609d759c"},
+    {file = "tifffile-2025.10.16.tar.gz", hash = "sha256:425179ec7837ac0e07bc95d2ea5bea9b179ce854967c12ba07fc3f093e58efc1"},
 ]
 
 [[package]]
@@ -2265,6 +2247,7 @@ name = "toolz"
 version = "0.12.1"
 requires_python = ">=3.7"
 summary = "List processing tools and functional utilities"
+groups = ["default"]
 files = [
     {file = "toolz-0.12.1-py3-none-any.whl", hash = "sha256:d22731364c07d72eea0a0ad45bafb2c2937ab6fd38a3507bf55eae8744aa7d85"},
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@@ -2275,6 +2258,7 @@ name = "tornado"
 version = "6.4.1"
 requires_python = ">=3.8"
 summary = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
+groups = ["default"]
 files = [
     {file = "tornado-6.4.1-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:163b0aafc8e23d8cdc3c9dfb24c5368af84a81e3364745ccb4427669bf84aec8"},
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@@ -2294,6 +2278,7 @@ name = "tqdm"
 version = "4.66.4"
 requires_python = ">=3.7"
 summary = "Fast, Extensible Progress Meter"
+groups = ["default"]
 dependencies = [
     "colorama; platform_system == \"Windows\"",
 ]
@@ -2304,15 +2289,16 @@ files = [
 
 [[package]]
 name = "trimesh"
-version = "4.4.1"
-requires_python = ">=3.7"
+version = "4.9.0"
+requires_python = ">=3.8"
 summary = "Import, export, process, analyze and view triangular meshes."
+groups = ["default"]
 dependencies = [
     "numpy>=1.20",
 ]
 files = [
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+    {file = "trimesh-4.9.0-py3-none-any.whl", hash = "sha256:934265a1de4b472bee21094c4e88d0a7522054b9911adb06e9b8062bb8757178"},
+    {file = "trimesh-4.9.0.tar.gz", hash = "sha256:ad907a223867f614ef1598d85a4c978845f39365cb7ccc93fa5800901fba3ef9"},
 ]
 
 [[package]]
@@ -2320,6 +2306,7 @@ name = "typing-extensions"
 version = "4.12.2"
 requires_python = ">=3.8"
 summary = "Backported and Experimental Type Hints for Python 3.8+"
+groups = ["default"]
 files = [
     {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
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@@ -2330,16 +2317,46 @@ name = "tzdata"
 version = "2024.1"
 requires_python = ">=2"
 summary = "Provider of IANA time zone data"
+groups = ["default"]
 files = [
     {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
     {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
 ]
 
+[[package]]
+name = "ujson"
+version = "5.11.0"
+requires_python = ">=3.9"
+summary = "Ultra fast JSON encoder and decoder for Python"
+groups = ["default"]
+marker = "python_version >= \"3.11\""
+files = [
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+    {file = "ujson-5.11.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:d8951bb7a505ab2a700e26f691bdfacf395bc7e3111e3416d325b513eea03a58"},
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+    {file = "ujson-5.11.0.tar.gz", hash = "sha256:e204ae6f909f099ba6b6b942131cee359ddda2b6e4ea39c12eb8b991fe2010e0"},
+]
+
 [[package]]
 name = "urllib3"
 version = "1.26.19"
 requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 summary = "HTTP library with thread-safe connection pooling, file post, and more."
+groups = ["default"]
 files = [
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@@ -2347,42 +2364,38 @@ files = [
 
 [[package]]
 name = "vtk"
-version = "9.3.1"
+version = "9.3.0"
 summary = "VTK is an open-source toolkit for 3D computer graphics, image processing, and visualization"
+groups = ["default"]
 dependencies = [
     "matplotlib>=2.0.0",
 ]
 files = [
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 ]
 
 [[package]]
-name = "wasmtime"
-version = "24.0.0"
+name = "wrapt"
+version = "1.17.3"
 requires_python = ">=3.8"
-summary = "A WebAssembly runtime powered by Wasmtime"
-dependencies = [
-    "importlib-resources>=5.10",
-]
+summary = "Module for decorators, wrappers and monkey patching."
+groups = ["default"]
 files = [
-    {file = "wasmtime-24.0.0-py3-none-any.whl", hash = "sha256:94799597e5067fb5d3c0d14fe2b06aff735a12eb4ed4389df5d2d449fa72a227"},
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+    {file = "wrapt-1.17.3-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:8cccf4f81371f257440c88faed6b74f1053eef90807b77e31ca057b2db74edb1"},
+    {file = "wrapt-1.17.3-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:d8a210b158a34164de8bb68b0e7780041a903d7b00c87e906fb69928bf7890d5"},
+    {file = "wrapt-1.17.3-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:79573c24a46ce11aab457b472efd8d125e5a51da2d1d24387666cd85f54c05b2"},
+    {file = "wrapt-1.17.3-cp311-cp311-win32.whl", hash = "sha256:c31eebe420a9a5d2887b13000b043ff6ca27c452a9a22fa71f35f118e8d4bf89"},
+    {file = "wrapt-1.17.3-cp311-cp311-win_amd64.whl", hash = "sha256:0b1831115c97f0663cb77aa27d381237e73ad4f721391a9bfb2fe8bc25fa6e77"},
+    {file = "wrapt-1.17.3-cp311-cp311-win_arm64.whl", hash = "sha256:5a7b3c1ee8265eb4c8f1b7d29943f195c00673f5ab60c192eba2d4a7eae5f46a"},
+    {file = "wrapt-1.17.3-py3-none-any.whl", hash = "sha256:7171ae35d2c33d326ac19dd8facb1e82e5fd04ef8c6c0e394d7af55a55051c22"},
+    {file = "wrapt-1.17.3.tar.gz", hash = "sha256:f66eb08feaa410fe4eebd17f2a2c8e2e46d3476e9f8c783daa8e09e0faa666d0"},
 ]
 
 [[package]]
@@ -2390,6 +2403,7 @@ name = "xarray"
 version = "2024.3.0"
 requires_python = ">=3.9"
 summary = "N-D labeled arrays and datasets in Python"
+groups = ["default"]
 dependencies = [
     "numpy>=1.23",
     "packaging>=22",
@@ -2405,6 +2419,7 @@ name = "xmlschema"
 version = "3.3.1"
 requires_python = ">=3.8"
 summary = "An XML Schema validator and decoder"
+groups = ["default"]
 dependencies = [
     "elementpath<5.0.0,>=4.4.0",
 ]
@@ -2418,6 +2433,7 @@ name = "xsdata"
 version = "24.3.1"
 requires_python = ">=3.8"
 summary = "Python XML Binding"
+groups = ["default"]
 dependencies = [
     "typing-extensions",
 ]
@@ -2431,6 +2447,7 @@ name = "yarl"
 version = "1.9.4"
 requires_python = ">=3.7"
 summary = "Yet another URL library"
+groups = ["default"]
 dependencies = [
     "idna>=2.0",
     "multidict>=4.0",
@@ -2503,18 +2520,20 @@ files = [
 
 [[package]]
 name = "zarr"
-version = "2.15.0"
-requires_python = ">=3.8"
+version = "3.1.3"
+requires_python = ">=3.11"
 summary = "An implementation of chunked, compressed, N-dimensional arrays for Python"
+groups = ["default"]
 dependencies = [
-    "asciitree",
-    "fasteners",
-    "numcodecs>=0.10.0",
-    "numpy>=1.20",
+    "donfig>=0.8",
+    "numcodecs[crc32c]>=0.14",
+    "numpy>=1.26",
+    "packaging>=22.0",
+    "typing-extensions>=4.9",
 ]
 files = [
-    {file = "zarr-2.15.0-py3-none-any.whl", hash = "sha256:7296b9f42cdc9096c5349527e71492c1b05ed5464027bfa5d008339796d00b9f"},
-    {file = "zarr-2.15.0.tar.gz", hash = "sha256:3894001c0bb5d68d3d21a0562cc49e6ba14fee7d17ad2be8d088ab301665a4c6"},
+    {file = "zarr-3.1.3-py3-none-any.whl", hash = "sha256:45f67f87f65f14fa453f99dd8110a5936b7ac69f3a21981d33e90407c80c302a"},
+    {file = "zarr-3.1.3.tar.gz", hash = "sha256:01342f3e26a02ed5670db608a5576fbdb8d76acb5c280bd2d0082454b1ba6f79"},
 ]
 
 [[package]]
@@ -2522,6 +2541,7 @@ name = "zict"
 version = "3.0.0"
 requires_python = ">=3.8"
 summary = "Mutable mapping tools"
+groups = ["default"]
 files = [
     {file = "zict-3.0.0-py2.py3-none-any.whl", hash = "sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae"},
     {file = "zict-3.0.0.tar.gz", hash = "sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5"},
@@ -2532,6 +2552,8 @@ name = "zipp"
 version = "3.19.2"
 requires_python = ">=3.8"
 summary = "Backport of pathlib-compatible object wrapper for zip files"
+groups = ["default"]
+marker = "python_version < \"3.12\""
 files = [
     {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
     {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
diff --git a/pyproject.toml b/pyproject.toml
index da99740..290e641 100755
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,26 +6,28 @@ authors = [
     {email = "cells@alleninstitute.org"},
 ]
 dependencies = [
+    "s3fs>=2025.9.0",
     "numpy<=1.26.4",
     "pandas>=2.0.0",
     "scipy>=1.13.1",
-    "bioio>=1.0.3",
-    "bioio-ome-tiff>=1.0.0",
-    "bioio-ome-zarr>=1.0.1",
+    "bioio>=3.0.0",
+    "bioio-ome-tiff>=1.4.0",
+    "bioio-ome-zarr>=3.0.3",
     "tqdm>=4.66.4",
     "matplotlib>=3.9.1",
     "seaborn>=0.13.2",
     "plotly>=5.23.0",
-    "trimesh>=4.1.0",
+    "cgal==6.0.1.post202410241521",
+    "trimesh>=4.9.0",
     "vtk==9.3.0",
     "point-cloud-utils==0.30.4",
     "pyvista>=0.43.10,<0.44",
-    "rtree>=1.3.0",
+    "rtree>=1.4.1",
     "scikit_posthocs>=0.9.0",
     "kaleido>=0.2.1,!=0.2.1.post1,<0.4.0",  # kaleido 0.2.1.post1 is published incorrectly
     "quilt3>=6.0.0",
 ]
-requires-python = ">=3.10,<3.12"
+requires-python = ">=3.11,<3.12"
 readme = "README.md"
 license = {file = "LICENSE"}