InterSCellar 0.1.0__tar.gz

interscellar-0.1.0/InterSCellar.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: InterSCellar
+Version: 0.1.0
+Summary: Surface-based Cell Neighbor Detection and Interscellar Volume Computation for 2D & 3D Spatial Omics
+Author-email: Eunice Yewon Lee <yl888@duke.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/euniceyl/InterSCellar
+Project-URL: Repository, https://github.com/euniceyl/InterSCellar
+Project-URL: Issues, https://github.com/euniceyl/InterSCellar/issues
+Keywords: spatial-omics,cell-neighbors,cell-interactions,cell-cell-communication,intercellular,single-cell,transcriptomics,proteomics,metabolomics,bioinformatics,computational-biology,visualization,3d
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: tqdm>=4.62.0
+Requires-Dist: opencv-python>=4.5.0
+Requires-Dist: dask[array]>=2021.0.0
+Requires-Dist: matplotlib>=3.4.0
+Requires-Dist: scikit-image>=0.18.0
+Requires-Dist: seaborn>=0.11.0
+Requires-Dist: napari>=0.4.0
+Requires-Dist: zarr>=2.10.0
+Requires-Dist: anndata>=0.8.0
+Requires-Dist: duckdb>=0.6.0
+Provides-Extra: anndata
+Requires-Dist: anndata>=0.8.0; extra == "anndata"
+Provides-Extra: duckdb
+Requires-Dist: duckdb>=0.6.0; extra == "duckdb"
+Provides-Extra: all
+Requires-Dist: anndata>=0.8.0; extra == "all"
+Requires-Dist: duckdb>=0.6.0; extra == "all"
+Dynamic: license-file
+
+# InterSCellar
+[![PyPI](https://img.shields.io/pypi/v/interscellar?logo=pypi&logoColor=blue)](https://pypi.org/project/interscellar/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+
+**InterSCellar** is a Python package for surface-Based cell neighborhood and interaction volume analysis in 3D spatial omics.
+
+![Package workflow](https://raw.githubusercontent.com/euniceyl/InterSCellar/main/docs/images/package_workflow.jpeg)
+
+## Installation
+
+**Install package:**
+```sh
+pip install interscellar
+```
+
+## Usage
+
+**Import:**
+```sh
+import interscellar
+```
+
+### 3D Pipeline:
+
+**(1) Cell Neighbor Detection & Graph Construction**
+```sh
+neighbors_3d, adata, conn = interscellar.find_cell_neighbors_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    metadata_csv_path="data/cell_metadata.csv",
+    max_distance_um=0.5,
+    voxel_size_um=(0.56, 0.28, 0.28),
+    n_jobs=4
+)
+```
+
+**(2) Interscellar Volume Computation**
+```sh
+# Interscellar volumes
+volumes_3d, adata, conn = interscellar.compute_interscellar_volumes_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    neighbor_pairs_csv="results/neighbors_3d.csv",
+    neighbor_db_path="/results/neighbor_graph.db",
+    voxel_size_um=(0.56, 0.28, 0.28),
+    max_distance_um=3.0,
+    intracellular_threshold_um=1.0,
+    n_jobs=4
+)
+```
+
+```sh
+# Cell-only volumes
+cellonly_3d = interscellar.compute_cell_only_volumes_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    interscellar_volumes_zarr="results/interscellar_volumes.zarr"
+)
+```
+
+### 2D Pipeline:
+
+**(1) Cell Neighbor Detection & Graph Construction**
+```sh
+neighbors_2d, adata, conn = interscellar.find_cell_neighbors_2d(
+    polygon_json_path="data/cell_polygons.json",
+    metadata_csv_path="data/cell_metadata.csv",
+    max_distance_um=1.0,
+    pixel_size_um=0.1085,
+    n_jobs=4
+)
+```
+
+### Utilities:
+
+**Volume Visualization**
+```sh
+# Full dataset (Napari)
+visualize-all-3d \
+  --cell-only-zarr "results/cell_only_volumes.zarr" \
+  --interscellar-zarr "results/interscellar_volumes.zarr" \
+  --cell-only-opacity 0.7 \
+  --interscellar-opacity 0.9
+```
+
+```sh
+# Single pair (Napari)
+visualize-pair-3d \
+  --pair-id 123 \
+  --cell-only-zarr "results/cell_only_volumes.zarr" \
+  --interscellar-zarr "results/interscellar_volumes.zarr" \
+  --pair-opacity 0.6 \
+  --cells-opacity 0.7
+```

interscellar-0.1.0/InterSCellar.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+InterSCellar.egg-info/PKG-INFO
+InterSCellar.egg-info/SOURCES.txt
+InterSCellar.egg-info/dependency_links.txt
+InterSCellar.egg-info/entry_points.txt
+InterSCellar.egg-info/requires.txt
+InterSCellar.egg-info/top_level.txt
+src/__init__.py
+src/api/__init__.py
+src/api/wrapper_2d.py
+src/api/wrapper_3d.py
+src/core/__init__.py
+src/core/compute_interscellar_volumes_3d.py
+src/core/find_cell_neighbors_2d.py
+src/core/find_cell_neighbors_3d.py
+src/visualization/__init__.py
+src/visualization/visualize_all_3d.py
+src/visualization/visualize_pair_3d.py

interscellar-0.1.0/InterSCellar.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

interscellar-0.1.0/InterSCellar.egg-info/entry_points.txt

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+[console_scripts]
+visualize-all-3d = interscellar.visualization.visualize_all_3d:main
+visualize-pair-3d = interscellar.visualization.visualize_pair_3d:main

interscellar-0.1.0/InterSCellar.egg-info/requires.txt

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+numpy>=1.20.0
+pandas>=1.3.0
+scipy>=1.7.0
+tqdm>=4.62.0
+opencv-python>=4.5.0
+dask[array]>=2021.0.0
+matplotlib>=3.4.0
+scikit-image>=0.18.0
+seaborn>=0.11.0
+napari>=0.4.0
+zarr>=2.10.0
+anndata>=0.8.0
+duckdb>=0.6.0
+
+[all]
+anndata>=0.8.0
+duckdb>=0.6.0
+
+[anndata]
+anndata>=0.8.0
+
+[duckdb]
+duckdb>=0.6.0

interscellar-0.1.0/InterSCellar.egg-info/top_level.txt

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+interscellar

interscellar-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Eunice Lee
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

interscellar-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: InterSCellar
+Version: 0.1.0
+Summary: Surface-based Cell Neighbor Detection and Interscellar Volume Computation for 2D & 3D Spatial Omics
+Author-email: Eunice Yewon Lee <yl888@duke.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/euniceyl/InterSCellar
+Project-URL: Repository, https://github.com/euniceyl/InterSCellar
+Project-URL: Issues, https://github.com/euniceyl/InterSCellar/issues
+Keywords: spatial-omics,cell-neighbors,cell-interactions,cell-cell-communication,intercellular,single-cell,transcriptomics,proteomics,metabolomics,bioinformatics,computational-biology,visualization,3d
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: tqdm>=4.62.0
+Requires-Dist: opencv-python>=4.5.0
+Requires-Dist: dask[array]>=2021.0.0
+Requires-Dist: matplotlib>=3.4.0
+Requires-Dist: scikit-image>=0.18.0
+Requires-Dist: seaborn>=0.11.0
+Requires-Dist: napari>=0.4.0
+Requires-Dist: zarr>=2.10.0
+Requires-Dist: anndata>=0.8.0
+Requires-Dist: duckdb>=0.6.0
+Provides-Extra: anndata
+Requires-Dist: anndata>=0.8.0; extra == "anndata"
+Provides-Extra: duckdb
+Requires-Dist: duckdb>=0.6.0; extra == "duckdb"
+Provides-Extra: all
+Requires-Dist: anndata>=0.8.0; extra == "all"
+Requires-Dist: duckdb>=0.6.0; extra == "all"
+Dynamic: license-file
+
+# InterSCellar
+[![PyPI](https://img.shields.io/pypi/v/interscellar?logo=pypi&logoColor=blue)](https://pypi.org/project/interscellar/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+
+**InterSCellar** is a Python package for surface-Based cell neighborhood and interaction volume analysis in 3D spatial omics.
+
+![Package workflow](https://raw.githubusercontent.com/euniceyl/InterSCellar/main/docs/images/package_workflow.jpeg)
+
+## Installation
+
+**Install package:**
+```sh
+pip install interscellar
+```
+
+## Usage
+
+**Import:**
+```sh
+import interscellar
+```
+
+### 3D Pipeline:
+
+**(1) Cell Neighbor Detection & Graph Construction**
+```sh
+neighbors_3d, adata, conn = interscellar.find_cell_neighbors_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    metadata_csv_path="data/cell_metadata.csv",
+    max_distance_um=0.5,
+    voxel_size_um=(0.56, 0.28, 0.28),
+    n_jobs=4
+)
+```
+
+**(2) Interscellar Volume Computation**
+```sh
+# Interscellar volumes
+volumes_3d, adata, conn = interscellar.compute_interscellar_volumes_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    neighbor_pairs_csv="results/neighbors_3d.csv",
+    neighbor_db_path="/results/neighbor_graph.db",
+    voxel_size_um=(0.56, 0.28, 0.28),
+    max_distance_um=3.0,
+    intracellular_threshold_um=1.0,
+    n_jobs=4
+)
+```
+
+```sh
+# Cell-only volumes
+cellonly_3d = interscellar.compute_cell_only_volumes_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    interscellar_volumes_zarr="results/interscellar_volumes.zarr"
+)
+```
+
+### 2D Pipeline:
+
+**(1) Cell Neighbor Detection & Graph Construction**
+```sh
+neighbors_2d, adata, conn = interscellar.find_cell_neighbors_2d(
+    polygon_json_path="data/cell_polygons.json",
+    metadata_csv_path="data/cell_metadata.csv",
+    max_distance_um=1.0,
+    pixel_size_um=0.1085,
+    n_jobs=4
+)
+```
+
+### Utilities:
+
+**Volume Visualization**
+```sh
+# Full dataset (Napari)
+visualize-all-3d \
+  --cell-only-zarr "results/cell_only_volumes.zarr" \
+  --interscellar-zarr "results/interscellar_volumes.zarr" \
+  --cell-only-opacity 0.7 \
+  --interscellar-opacity 0.9
+```
+
+```sh
+# Single pair (Napari)
+visualize-pair-3d \
+  --pair-id 123 \
+  --cell-only-zarr "results/cell_only_volumes.zarr" \
+  --interscellar-zarr "results/interscellar_volumes.zarr" \
+  --pair-opacity 0.6 \
+  --cells-opacity 0.7
+```

interscellar-0.1.0/README.md

@@ -0,0 +1,91 @@
+# InterSCellar
+[![PyPI](https://img.shields.io/pypi/v/interscellar?logo=pypi&logoColor=blue)](https://pypi.org/project/interscellar/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+
+**InterSCellar** is a Python package for surface-Based cell neighborhood and interaction volume analysis in 3D spatial omics.
+
+![Package workflow](https://raw.githubusercontent.com/euniceyl/InterSCellar/main/docs/images/package_workflow.jpeg)
+
+## Installation
+
+**Install package:**
+```sh
+pip install interscellar
+```
+
+## Usage
+
+**Import:**
+```sh
+import interscellar
+```
+
+### 3D Pipeline:
+
+**(1) Cell Neighbor Detection & Graph Construction**
+```sh
+neighbors_3d, adata, conn = interscellar.find_cell_neighbors_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    metadata_csv_path="data/cell_metadata.csv",
+    max_distance_um=0.5,
+    voxel_size_um=(0.56, 0.28, 0.28),
+    n_jobs=4
+)
+```
+
+**(2) Interscellar Volume Computation**
+```sh
+# Interscellar volumes
+volumes_3d, adata, conn = interscellar.compute_interscellar_volumes_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    neighbor_pairs_csv="results/neighbors_3d.csv",
+    neighbor_db_path="/results/neighbor_graph.db",
+    voxel_size_um=(0.56, 0.28, 0.28),
+    max_distance_um=3.0,
+    intracellular_threshold_um=1.0,
+    n_jobs=4
+)
+```
+
+```sh
+# Cell-only volumes
+cellonly_3d = interscellar.compute_cell_only_volumes_3d(
+    ome_zarr_path="data/segmentation.zarr",
+    interscellar_volumes_zarr="results/interscellar_volumes.zarr"
+)
+```
+
+### 2D Pipeline:
+
+**(1) Cell Neighbor Detection & Graph Construction**
+```sh
+neighbors_2d, adata, conn = interscellar.find_cell_neighbors_2d(
+    polygon_json_path="data/cell_polygons.json",
+    metadata_csv_path="data/cell_metadata.csv",
+    max_distance_um=1.0,
+    pixel_size_um=0.1085,
+    n_jobs=4
+)
+```
+
+### Utilities:
+
+**Volume Visualization**
+```sh
+# Full dataset (Napari)
+visualize-all-3d \
+  --cell-only-zarr "results/cell_only_volumes.zarr" \
+  --interscellar-zarr "results/interscellar_volumes.zarr" \
+  --cell-only-opacity 0.7 \
+  --interscellar-opacity 0.9
+```
+
+```sh
+# Single pair (Napari)
+visualize-pair-3d \
+  --pair-id 123 \
+  --cell-only-zarr "results/cell_only_volumes.zarr" \
+  --interscellar-zarr "results/interscellar_volumes.zarr" \
+  --pair-opacity 0.6 \
+  --cells-opacity 0.7
+```

interscellar-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "InterSCellar"
+version = "0.1.0"
+description = "Surface-based Cell Neighbor Detection and Interscellar Volume Computation for 2D & 3D Spatial Omics"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "MIT"}
+authors = [
+    {name = "Eunice Yewon Lee", email = "yl888@duke.edu"}
+]
+keywords = [
+    "spatial-omics",
+    "cell-neighbors",
+    "cell-interactions",
+    "cell-cell-communication",
+    "intercellular",
+    "single-cell",
+    "transcriptomics",
+    "proteomics",
+    "metabolomics",
+    "bioinformatics",
+    "computational-biology",
+    "visualization",
+    "3d"
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+    "numpy>=1.20.0",
+    "pandas>=1.3.0",
+    "scipy>=1.7.0",
+    "tqdm>=4.62.0",
+    "opencv-python>=4.5.0",
+    "dask[array]>=2021.0.0",
+    "matplotlib>=3.4.0",
+    "scikit-image>=0.18.0",
+    "seaborn>=0.11.0",
+    "napari>=0.4.0",
+    "zarr>=2.10.0",
+    "anndata>=0.8.0",
+    "duckdb>=0.6.0",
+]
+
+[project.optional-dependencies]
+anndata = [
+    "anndata>=0.8.0",
+]
+duckdb = [
+    "duckdb>=0.6.0",
+]
+all = [
+    "anndata>=0.8.0",
+    "duckdb>=0.6.0",
+]
+
+[project.scripts]
+visualize-all-3d = "interscellar.visualization.visualize_all_3d:main"
+visualize-pair-3d = "interscellar.visualization.visualize_pair_3d:main"
+
+[project.urls]
+Homepage = "https://github.com/euniceyl/InterSCellar"
+Repository = "https://github.com/euniceyl/InterSCellar"
+Issues = "https://github.com/euniceyl/InterSCellar/issues"
+
+[tool.setuptools]
+package-dir = {"interscellar" = "src"}
+packages = ["interscellar", "interscellar.api", "interscellar.core", "interscellar.visualization"]
+
+[tool.setuptools.package-data]
+"*" = ["*.py", "*.md", "LICENSE"]
+

interscellar-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

interscellar-0.1.0/src/__init__.py

@@ -0,0 +1,22 @@
+__version__ = "0.1.0"
+
+from .api import (
+    find_cell_neighbors_2d,
+    find_cell_neighbors_3d,
+    compute_interscellar_volumes_3d,
+    compute_cell_only_volumes_3d
+)
+
+from .visualization import (
+    visualize_all_3d,
+    visualize_pair_3d
+)
+
+__all__ = [
+    "find_cell_neighbors_2d",
+    "find_cell_neighbors_3d",
+    "compute_interscellar_volumes_3d",
+    "compute_cell_only_volumes_3d",
+    "visualize_all_3d",
+    "visualize_pair_3d",
+]

interscellar-0.1.0/src/api/__init__.py

@@ -0,0 +1,14 @@
+from .wrapper_2d import find_cell_neighbors_2d
+from .wrapper_3d import (
+    find_cell_neighbors_3d,
+    compute_interscellar_volumes_3d,
+    compute_cell_only_volumes_3d
+)
+
+__all__ = [
+    "find_cell_neighbors_2d",
+    "find_cell_neighbors_3d",
+    "compute_interscellar_volumes_3d",
+    "compute_cell_only_volumes_3d",
+]
+