sphero-vem 0.1.0__tar.gz

sphero_vem-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Davide Bottone
+
+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.

sphero_vem-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sphero-vem
+Version: 0.1.0
+Summary: Quantitative 3D analysis of volume electron microscopy data with ML and classical image processing
+License: MIT License
+         
+         Copyright (c) 2026 Davide Bottone
+         
+         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.
+License-File: LICENSE
+Author: Davide Bottone
+Author-email: d.bottone@pm.me
+Requires-Python: >=3.12,<3.14
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Operating System :: OS Independent
+Provides-Extra: cuda
+Requires-Dist: careamics (>=0.0.9)
+Requires-Dist: cellpose (>=4.0.3,<5.0.0)
+Requires-Dist: cucim-cu12 (>=25.12.0,<26.0.0) ; extra == "cuda"
+Requires-Dist: cupy-cuda12x (>=13.6.0,<14.0.0) ; extra == "cuda"
+Requires-Dist: dacite (>=1.9.2,<2.0.0)
+Requires-Dist: dask-image (>=2025.11.0,<2026.0.0)
+Requires-Dist: dotenv (>=0.9.9,<0.10.0)
+Requires-Dist: kornia (>=0.8.0,<0.9.0)
+Requires-Dist: lightning (>=2.5.1,<3.0.0)
+Requires-Dist: numpy (>=2.0.0,<3.0.0)
+Requires-Dist: pandas (>=2.3.0,<3.0.0)
+Requires-Dist: polars (>=1.39.2,<2.0.0)
+Requires-Dist: scikit-learn (>=1.6.1,<2.0.0)
+Requires-Dist: torch (>=2.0.0,<2.7.0)
+Requires-Dist: torchvision (>=0.15.0,<0.22.0)
+Requires-Dist: wandb (>=0.19.10,<0.20.0)
+Requires-Dist: zarr (>=3.0.0,<4.0.0)
+Project-URL: Documentation, https://dv-bt.github.io/sphero-vem/
+Project-URL: Homepage, https://dv-bt.github.io/sphero-vem/
+Project-URL: Repository, https://github.com/dv-bt/sphero-vem/
+Description-Content-Type: text/markdown
+
+# sphero-vem
+
+[![Python](https://img.shields.io/badge/python-3.12%20%7C%203.13-blue)](https://www.python.org)
+[![CI](https://github.com/dv-bt/sphero-vem/actions/workflows/ci.yml/badge.svg)](https://github.com/dv-bt/sphero-vem/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/dv-bt/sphero-vem/graph/badge.svg?token=0VqxCn7LKp)](https://codecov.io/gh/dv-bt/sphero-vem)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+
+Python library for quantitative analysis of volumetric electron microscopy (vEM) data.
+
+`sphero-vem` was developed for the end-to-end analysis pipeline described in:
+
+> Bottone et al., *3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy*, [Preprint: [https://doi.org/10.64898/2026.04.17.719153](https://doi.org/10.64898/2026.04.17.719153)]
+
+While the library was originally developed for SBF-SEM data of nanoparticle-loaded tumor spheroids, the individual components are designed to be reusable for other vEM datasets and workflows.
+
+## Capabilities
+
+- **Denoising**: self-supervised Noise2Void via CAREamics on large zarr volumes
+- **Registration**: intensity-based pairwise slice alignment with multi-resolution PyTorch optimization
+- **Segmentation**: fine-tuning and inference with Cellpose-SAM for cells and nuclei; empirical Bayes approach for nanoparticles
+- **Shape analysis**: 3D morphological descriptors via signed distance functions and mesh-based curvature (mean curvature, curvedness, shape index, fractal dimension)
+- **Spatial analysis**: nanoparticle-to-nucleus distance quantification per cell
+- **Data management**: zarr-native I/O with OME-NGFF multiscale support and processing metadata tracking
+
+## Installation
+
+Clone the repository and install with [Poetry](https://python-poetry.org/):
+
+```bash
+git clone https://github.com/dv-bt/sphero-vem.git
+cd sphero-vem
+poetry install           # CPU and limited GPU acceleration
+poetry install -E cuda   # with full CUDA 12.x GPU acceleration (Linux/Windows only)
+```
+
+## Documentation
+
+Full documentation is available on the [official website](https://dv-bt.github.io/sphero-vem/).
+
+## Requirements
+
+- Python 3.12–3.13
+- [PyTorch](https://pytorch.org/) ≥ 2.0
+- [NumPy](https://numpy.org/) ≥ 2.0
+- [zarr](https://zarr.readthedocs.io/) ≥ 3.0
+- [Cellpose](https://cellpose.readthedocs.io/) ≥ 4.0
+- [CAREamics](https://careamics.github.io/) ≥ 0.0.9
+
+## GPU acceleration
+
+PyTorch-based stages (denoising, registration, Cellpose segmentation) support GPU execution via PyTorch's native device management, including CUDA and MPS (Apple Silicon), and require no additional dependencies.
+
+Array operation stages (nanoparticle segmentation, shape analysis, spatial analysis) additionally support CUDA acceleration via CuPy and CuCIM, installed with the `cuda` optional dependency group above. GPU acceleration is handled automatically with a custom orchestrator.
+
+## Dataset and model weights
+
+The annotated SBF-SEM dataset used to develop this pipeline is available at BioImage Archive (https://doi.org/10.6019/S-BIAD3263). Fine-tuned Cellpose-SAM model weights are available on Zenodo (https://doi.org/10.5281/zenodo.19616546).
+
+## Citation
+
+If you use this library, please cite the accompanying paper:
+
+```bibtex
+@article {Bottone2026,
+	author = {Bottone, Davide and Gerken, Lukas RH and Habermann, Sebastian and Mateos, Jose Maria and Lucas, Miriam S and Riemann, Johannes and Fachet, Melanie and Resch-Genger, Ute and Kissling, Vera M and Roesslein, Matthias and Gogos, Alexander and Herrmann, Inge K},
+	title = {3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy},
+	year = {2026},
+	doi = {10.64898/2026.04.17.719153},
+	eprint = {https://www.biorxiv.org/content/early/2026/04/21/2026.04.17.719153},
+}
+```
+
+## License
+
+See [LICENSE](LICENSE) for details.
+

sphero_vem-0.1.0/README.md

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+# sphero-vem
+
+[![Python](https://img.shields.io/badge/python-3.12%20%7C%203.13-blue)](https://www.python.org)
+[![CI](https://github.com/dv-bt/sphero-vem/actions/workflows/ci.yml/badge.svg)](https://github.com/dv-bt/sphero-vem/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/dv-bt/sphero-vem/graph/badge.svg?token=0VqxCn7LKp)](https://codecov.io/gh/dv-bt/sphero-vem)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+
+Python library for quantitative analysis of volumetric electron microscopy (vEM) data.
+
+`sphero-vem` was developed for the end-to-end analysis pipeline described in:
+
+> Bottone et al., *3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy*, [Preprint: [https://doi.org/10.64898/2026.04.17.719153](https://doi.org/10.64898/2026.04.17.719153)]
+
+While the library was originally developed for SBF-SEM data of nanoparticle-loaded tumor spheroids, the individual components are designed to be reusable for other vEM datasets and workflows.
+
+## Capabilities
+
+- **Denoising**: self-supervised Noise2Void via CAREamics on large zarr volumes
+- **Registration**: intensity-based pairwise slice alignment with multi-resolution PyTorch optimization
+- **Segmentation**: fine-tuning and inference with Cellpose-SAM for cells and nuclei; empirical Bayes approach for nanoparticles
+- **Shape analysis**: 3D morphological descriptors via signed distance functions and mesh-based curvature (mean curvature, curvedness, shape index, fractal dimension)
+- **Spatial analysis**: nanoparticle-to-nucleus distance quantification per cell
+- **Data management**: zarr-native I/O with OME-NGFF multiscale support and processing metadata tracking
+
+## Installation
+
+Clone the repository and install with [Poetry](https://python-poetry.org/):
+
+```bash
+git clone https://github.com/dv-bt/sphero-vem.git
+cd sphero-vem
+poetry install           # CPU and limited GPU acceleration
+poetry install -E cuda   # with full CUDA 12.x GPU acceleration (Linux/Windows only)
+```
+
+## Documentation
+
+Full documentation is available on the [official website](https://dv-bt.github.io/sphero-vem/).
+
+## Requirements
+
+- Python 3.12–3.13
+- [PyTorch](https://pytorch.org/) ≥ 2.0
+- [NumPy](https://numpy.org/) ≥ 2.0
+- [zarr](https://zarr.readthedocs.io/) ≥ 3.0
+- [Cellpose](https://cellpose.readthedocs.io/) ≥ 4.0
+- [CAREamics](https://careamics.github.io/) ≥ 0.0.9
+
+## GPU acceleration
+
+PyTorch-based stages (denoising, registration, Cellpose segmentation) support GPU execution via PyTorch's native device management, including CUDA and MPS (Apple Silicon), and require no additional dependencies.
+
+Array operation stages (nanoparticle segmentation, shape analysis, spatial analysis) additionally support CUDA acceleration via CuPy and CuCIM, installed with the `cuda` optional dependency group above. GPU acceleration is handled automatically with a custom orchestrator.
+
+## Dataset and model weights
+
+The annotated SBF-SEM dataset used to develop this pipeline is available at BioImage Archive (https://doi.org/10.6019/S-BIAD3263). Fine-tuned Cellpose-SAM model weights are available on Zenodo (https://doi.org/10.5281/zenodo.19616546).
+
+## Citation
+
+If you use this library, please cite the accompanying paper:
+
+```bibtex
+@article {Bottone2026,
+	author = {Bottone, Davide and Gerken, Lukas RH and Habermann, Sebastian and Mateos, Jose Maria and Lucas, Miriam S and Riemann, Johannes and Fachet, Melanie and Resch-Genger, Ute and Kissling, Vera M and Roesslein, Matthias and Gogos, Alexander and Herrmann, Inge K},
+	title = {3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy},
+	year = {2026},
+	doi = {10.64898/2026.04.17.719153},
+	eprint = {https://www.biorxiv.org/content/early/2026/04/21/2026.04.17.719153},
+}
+```
+
+## License
+
+See [LICENSE](LICENSE) for details.

sphero_vem-0.1.0/pyproject.toml

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+[project]
+name = "sphero-vem"
+version = "0.1.0"
+description = "Quantitative 3D analysis of volume electron microscopy data with ML and classical image processing"
+authors = [
+    {name = "Davide Bottone",email = "d.bottone@pm.me"}
+]
+readme = "README.md"
+license = {file = "LICENSE"}
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Image Processing",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Operating System :: OS Independent",
+]
+requires-python = ">=3.12,<3.14"
+dependencies = [
+    "numpy (>=2.0.0,<3.0.0)",
+    "zarr (>=3.0.0,<4.0.0)",
+    "torch (>=2.0.0,<2.7.0)",
+    "torchvision (>=0.15.0,<0.22.0)",
+    "careamics (>=0.0.9)",
+    "kornia (>=0.8.0,<0.9.0)",
+    "lightning (>=2.5.1,<3.0.0)",
+    "dotenv (>=0.9.9,<0.10.0)",
+    "cellpose (>=4.0.3,<5.0.0)",
+    "scikit-learn (>=1.6.1,<2.0.0)",
+    "pandas (>=2.3.0,<3.0.0)",
+    "dask-image (>=2025.11.0,<2026.0.0)",
+    "dacite (>=1.9.2,<2.0.0)",
+    "polars (>=1.39.2,<2.0.0)",
+    "wandb (>=0.19.10,<0.20.0)",
+]
+
+[project.urls]
+  Homepage = "https://dv-bt.github.io/sphero-vem/"
+  Repository = "https://github.com/dv-bt/sphero-vem/"
+  Documentation = "https://dv-bt.github.io/sphero-vem/"
+
+[project.optional-dependencies]
+cuda = [
+    "cupy-cuda12x>=13.6.0,<14.0.0",
+    "cucim-cu12>=25.12.0,<26.0.0",
+]
+
+[tool.poetry]
+packages = [{include = "sphero_vem", from = "src"}]
+
+[tool.poetry.group.dev]
+optional = true
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.3.5"
+pytest-cov = "^6.1.1"
+ruff = "^0.11.4"
+pre-commit = "^4.2.0"
+bumpver = "^2025.1131"
+
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.docs.dependencies]
+sphinx = "^8.0.0"
+pydata-sphinx-theme = "^0.16.0"
+sphinx-autodoc-typehints = "^3.0.0"
+
+[tool.poetry.group.napari]
+optional = true
+
+[tool.poetry.group.napari.dependencies]
+napari = {extras = ["pyqt6"], version = "^0.6.6"}
+
+[tool.poetry.group.notebook]
+optional = true
+
+[tool.poetry.group.notebook.dependencies]
+ipykernel = "^6.29.5"
+ipympl = "^0.9.7"
+seaborn = "^0.13.2"
+statannotations = ">=0.7.2,<0.8.0"
+statsmodels = ">=0.14.6,<0.15.0"
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.bumpver]
+current_version = "0.1.0"
+version_pattern = "MAJOR.MINOR.PATCH"
+commit_message = "Bump version: {old_version} -> {new_version}"
+tag_message = "{new_version}"
+commit = true
+tag = true
+push = true
+
+[tool.bumpver.file_patterns]
+"pyproject.toml" = [
+    'version = "{version}"',
+]

sphero_vem-0.1.0/src/sphero_vem/__init__.py

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+"""
+sphero-vem: 3D Volumetric Analysis Tools for Electron Microscopy
+
+A scientific Python package for processing, registering, segmenting, and analyzing
+3D volumetric microscopy data, with focus on spheroid cell cultures and electron
+microscopy imaging.
+"""
+
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("sphero-vem")
+except PackageNotFoundError:
+    __version__ = "unknown"
+
+# Core I/O operations
+from .io import (
+    write_image,
+    stack_to_zarr,
+    write_zarr,
+)
+
+# Preprocessing
+from .preprocessing import (
+    downscale_tensor,
+)
+
+# Registration
+from .registration import (
+    RegistrationConfig,
+    register_image_pair,
+    register_stack,
+    TransformType,
+)
+
+# Denoising
+from .denoising import (
+    DenoisingConfig,
+    train_n2v,
+    denoise_stack,
+)
+
+# Measurement
+from .measure import (
+    LabelAnalysisConfig,
+    props_voxel,
+    props_sdf,
+    props_mesh,
+    props_fractal,
+    label_properties,
+    analyze_labels,
+    save_regionprops,
+    read_regionprops,
+    get_mesh,
+)
+
+# Segmentation
+from .segmentation.cellpose import (
+    CellposeFlowConfig,
+    calculate_flows,
+    calculate_masks,
+)
+
+# Utilities
+from .utils import (
+    BaseConfig,
+    ProcessingStep,
+    timestamp,
+    detect_torch_device,
+)
+
+__all__ = [
+    # Version
+    "__version__",
+    # I/O
+    "write_image",
+    "stack_to_zarr",
+    "write_zarr",
+    # Preprocessing
+    "downscale_tensor",
+    # Registration
+    "RegistrationConfig",
+    "register_image_pair",
+    "register_stack",
+    "TransformType",
+    # Denoising
+    "DenoisingConfig",
+    "train_n2v",
+    "denoise_stack",
+    # Measurement
+    "LabelAnalysisConfig",
+    "props_voxel",
+    "props_sdf",
+    "props_mesh",
+    "props_fractal",
+    "label_properties",
+    "analyze_labels",
+    "save_regionprops",
+    "read_regionprops",
+    "get_mesh",
+    # Segmentation
+    "CellposeFlowConfig",
+    "calculate_flows",
+    "calculate_masks",
+    # Utilities
+    "BaseConfig",
+    "ProcessingStep",
+    "timestamp",
+    "detect_torch_device",
+]