sainsc 0.1.0__tar.gz

sainsc-0.1.0/Cargo.toml

@@ -0,0 +1,23 @@
+[package]
+name    = "_utils_rust"
+version = "0.1.0"
+edition = "2021"
+
+[lib]
+name       = "_utils_rust"
+crate-type = ["cdylib"]
+
+[dependencies]
+bincode       = { version = "1.3" }
+indexmap      = { version = "2.1.0", features = ["rayon"] }
+itertools     = { version = "0.12.1" }
+ndarray       = { version = "0.15.6", features = ["rayon"] }
+ndarray-stats = { version = "0.5.1" }
+num           = { version = "0.4.1" }
+numpy         = { version = "0.21.0" }
+polars        = { version = "0.41", features = ["partition_by", "dtype-categorical"] }
+polars-arrow  = { version = "0.41" }
+pyo3          = { version = "0.21.0", features = ["extension-module"] }
+pyo3-polars   = { version = "0.15.0" }
+rayon         = { version = "1.8.0" }
+sprs          = { version = "0.11.1", features = ["serde"] }

sainsc-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Niklas Müller-Bötticher, Naveed Ishaque, Roland Eils, Berlin Institute of Health @ Charité
+
+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.

sainsc-0.1.0/MANIFEST.in

@@ -0,0 +1,11 @@
+# setuptools-scm includes all tracked files by default in sdist
+
+# exclude docs as it contains large files
+prune docs
+
+# exclude unnecessary configs
+exclude .pre-commit-config.yaml .readthedocs.yaml .yamlfmt.yaml
+prune .github
+
+# exclude example data
+prune data

sainsc-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: sainsc
+Version: 0.1.0
+Summary: Segmentation-free Analysis of In Situ Capture data
+Author-email: Niklas Müller-Bötticher <niklas.mueller-boetticher@charite.de>
+License: MIT License
+        
+        Copyright (c) 2024 Niklas Müller-Bötticher, Naveed Ishaque, Roland Eils, Berlin Institute of Health @ Charité
+        
+        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.
+        
+Project-URL: homepage, https://github.com/HiDiHlabs/sainsc
+Project-URL: documentation, https://sainsc.readthedocs.io
+Project-URL: repository, https://github.com/HiDiHlabs/sainsc
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: anndata>=0.9
+Requires-Dist: matplotlib
+Requires-Dist: matplotlib-scalebar
+Requires-Dist: numba>=0.44
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas
+Requires-Dist: polars[pandas]>=1
+Requires-Dist: scikit-image>=0.18
+Requires-Dist: scipy>=1.9
+Requires-Dist: seaborn>=0.11
+Provides-Extra: spatialdata
+Requires-Dist: spatialdata>=0.1; extra == "spatialdata"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-autoapi>=3.1; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: myst-nb; extra == "docs"
+Provides-Extra: data
+Requires-Dist: pooch>=1; extra == "data"
+Provides-Extra: dev
+Requires-Dist: sainsc[data,docs,spatialdata]; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+
+# sainsc
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Code style: 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)
+[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+
+/ˈsaiəns/
+
+_"**S**egmentation-free **A**nalysis of **In S**itu **C**apture data"_
+or alternatively
+"_**S**tupid **A**cronyms **In Sc**ience_"
+
+`sainsc` is a segmentation-free analysis tool for spatial transcriptomics from in situ
+capture technologies (but also works for imaging-based technologies). It is easily
+integratable with the [scverse](https://github.com/scverse) (i.e. `scanpy` and `squidpy`)
+by exporting data in [`AnnData`](https://anndata.readthedocs.io/) or
+[`SpatialData`](https://spatialdata.scverse.org/) format.
+
+## Installation
+
+`sainsc` will be made available on [PyPI](https://pypi.org/) and
+[bioconda](https://bioconda.github.io/). For detailed installation instructions
+please refer to the [documentation](https://sainsc.readthedocs.io/en/stable/installation.html).
+
+## Documentation
+
+For an extensive documentation of the package please refer to the
+[ReadTheDocs page](https://sainsc.readthedocs.io)
+
+## Versioning
+
+This project follows the [SemVer](https://semver.org/) guidelines for versioning.
+
+## Citations
+
+If you are using `sainsc` for your research please cite
+
+Müller-Bötticher, N., Tiesmeyer, S., Eils, R., and Ishaque, N.
+"Sainsc: a computational tool for segmentation-free analysis of in-situ capture"
+bioRxiv (2024) https://doi.org/10.1101/2024.08.02.603879
+
+## License
+
+This project is licensed under the MIT License - for details please refer to the
+[LICENSE](./LICENSE) file.

sainsc-0.1.0/README.md

@@ -0,0 +1,48 @@
+# sainsc
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Code style: 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)
+[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+
+/ˈsaiəns/
+
+_"**S**egmentation-free **A**nalysis of **In S**itu **C**apture data"_
+or alternatively
+"_**S**tupid **A**cronyms **In Sc**ience_"
+
+`sainsc` is a segmentation-free analysis tool for spatial transcriptomics from in situ
+capture technologies (but also works for imaging-based technologies). It is easily
+integratable with the [scverse](https://github.com/scverse) (i.e. `scanpy` and `squidpy`)
+by exporting data in [`AnnData`](https://anndata.readthedocs.io/) or
+[`SpatialData`](https://spatialdata.scverse.org/) format.
+
+## Installation
+
+`sainsc` will be made available on [PyPI](https://pypi.org/) and
+[bioconda](https://bioconda.github.io/). For detailed installation instructions
+please refer to the [documentation](https://sainsc.readthedocs.io/en/stable/installation.html).
+
+## Documentation
+
+For an extensive documentation of the package please refer to the
+[ReadTheDocs page](https://sainsc.readthedocs.io)
+
+## Versioning
+
+This project follows the [SemVer](https://semver.org/) guidelines for versioning.
+
+## Citations
+
+If you are using `sainsc` for your research please cite
+
+Müller-Bötticher, N., Tiesmeyer, S., Eils, R., and Ishaque, N.
+"Sainsc: a computational tool for segmentation-free analysis of in-situ capture"
+bioRxiv (2024) https://doi.org/10.1101/2024.08.02.603879
+
+## License
+
+This project is licensed under the MIT License - for details please refer to the
+[LICENSE](./LICENSE) file.

sainsc-0.1.0/pyproject.toml

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+[build-system]
+requires      = ["setuptools>=61.0.0", "setuptools_scm[toml]>=6.2", "setuptools-rust>=1.7"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name            = "sainsc"
+description     = "Segmentation-free Analysis of In Situ Capture data"
+readme          = { file = "README.md", content-type = "text/markdown" }
+license         = { file = "LICENSE" }
+requires-python = ">=3.10"
+dynamic         = ["version"]
+
+authors = [
+    { name = "Niklas Müller-Bötticher", email = "niklas.mueller-boetticher@charite.de" },
+]
+dependencies = [
+    "anndata>=0.9",
+    "matplotlib",
+    "matplotlib-scalebar",
+    "numba>=0.44",
+    "numpy>=1.21",
+    "pandas",
+    "polars[pandas]>=1",
+    "scikit-image>=0.18",
+    "scipy>=1.9",
+    "seaborn>=0.11",
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Rust",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Typing :: Typed",
+]
+
+[project.optional-dependencies]
+spatialdata = ["spatialdata>=0.1"]
+docs = [
+    "sphinx",
+    "sphinx-autoapi>=3.1",
+    "sphinx-copybutton",
+    "sphinx-rtd-theme",
+    "myst-nb",
+]
+data = ["pooch>=1"]
+dev = ["sainsc[data,docs,spatialdata]", "pre-commit"]
+
+[project.urls]
+homepage      = "https://github.com/HiDiHlabs/sainsc"
+documentation = "https://sainsc.readthedocs.io"
+repository    = "https://github.com/HiDiHlabs/sainsc"
+
+
+[tool]
+
+[tool.setuptools]
+zip-safe = false
+
+[tool.setuptools.packages.find]
+include = ["sainsc", "sainsc.io", "sainsc.lazykde", "sainsc.utils"]
+
+[tool.setuptools_scm]
+
+[[tool.setuptools-rust.ext-modules]]
+target = "sainsc._utils_rust"
+
+[tool.isort]
+profile = "black"
+
+[tool.black]
+target-version = ["py310", "py311", "py312"]
+
+[tool.ruff]
+target-version = "py310"
+
+[tool.mypy]
+python_version         = "3.10"
+ignore_missing_imports = true
+warn_no_return         = false
+packages               = "sainsc"
+plugins                = "numpy.typing.mypy_plugin"
+
+[tool.codespell]
+ignore-words-list = "coo,crate"
+
+[tool.cibuildwheel]
+archs = 'auto64'
+# build = 'cp310-*'
+skip = "pp*" # skip PyPy
+
+[tool.cibuildwheel.linux]
+# cibuildwheel runs linux in containers so we need to install rust there
+before-all  = "curl -sSf https://sh.rustup.rs | sh -s -- --default-toolchain stable -y"
+environment = { PATH = "$PATH:$HOME/.cargo/bin" }

sainsc-0.1.0/sainsc/__init__.py

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+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("sainsc")
+except PackageNotFoundError:
+    __version__ = "unknown version"
+
+from ._utils_rust import GridCounts
+from .io import read_StereoSeq, read_StereoSeq_bins
+from .lazykde import LazyKDE, gaussian_kernel
+
+__all__ = [
+    "GridCounts",
+    "LazyKDE",
+    "gaussian_kernel",
+    "read_StereoSeq",
+    "read_StereoSeq_bins",
+]

sainsc-0.1.0/sainsc/_typealias.py

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+import os
+from typing import TypeAlias
+
+import numpy as np
+from numpy.typing import NDArray
+from scipy.sparse import csc_array, csc_matrix, csr_array, csr_matrix
+
+_PathLike: TypeAlias = os.PathLike[str] | str
+
+_Csr: TypeAlias = csr_array | csr_matrix
+_Csc: TypeAlias = csc_array | csc_matrix
+_Csx: TypeAlias = _Csr | _Csc
+_CsxArray: TypeAlias = csc_array | csr_array
+
+_RangeTuple: TypeAlias = tuple[int, int]
+_RangeTuple2D: TypeAlias = tuple[_RangeTuple, _RangeTuple]
+
+_Local_Max: TypeAlias = tuple[NDArray[np.int_], NDArray[np.int_]]
+
+_Color: TypeAlias = str | tuple[float, float, float]
+_Cmap: TypeAlias = str | list[_Color] | dict[str, _Color]

sainsc-0.1.0/sainsc/_utils.py

@@ -0,0 +1,45 @@
+import os
+from typing import NoReturn
+
+import numpy as np
+import pandas as pd
+from numpy.typing import NDArray
+
+from ._utils_rust import coordinate_as_string
+
+
+def _get_n_cpus() -> int:
+    return len(os.sched_getaffinity(0))
+
+
+def _get_coordinate_index(
+    x: NDArray[np.integer],
+    y: NDArray[np.integer],
+    *,
+    name: str | None = None,
+    n_threads: int = 1,
+) -> pd.Index:
+    x_i32: NDArray[np.int32] = x.astype(np.int32, copy=False)
+    y_i32: NDArray[np.int32] = y.astype(np.int32, copy=False)
+
+    return pd.Index(
+        coordinate_as_string(x_i32, y_i32, n_threads=n_threads), dtype=str, name=name
+    )
+
+
+def _bin_coordinates(df: pd.DataFrame, bin_size: float) -> pd.DataFrame:
+    df = df.assign(
+        x=lambda df: _get_bin_coordinate(df["x"].to_numpy(), bin_size),
+        y=lambda df: _get_bin_coordinate(df["y"].to_numpy(), bin_size),
+    )
+    return df
+
+
+def _get_bin_coordinate(coor: NDArray[np.number], bin_size: float) -> NDArray[np.int32]:
+    return np.floor(coor / bin_size).astype(np.int32, copy=False)
+
+
+def _raise_module_load_error(e: Exception, fn: str, pkg: str, extra: str) -> NoReturn:
+    raise ModuleNotFoundError(
+        f"`{fn}` requires '{pkg}' to be installed, e.g. via the '{extra}' extra."
+    ) from e

sainsc-0.1.0/sainsc/_utils_rust.pyi

@@ -0,0 +1,267 @@
+import numpy as np
+from numpy.typing import NDArray
+from polars import DataFrame
+
+from ._typealias import _Csx, _CsxArray
+
+def sparse_kde_csx_py(
+    counts: _Csx, kernel: NDArray[np.float32], *, threshold: float = 0
+) -> _CsxArray:
+    """
+    Calculate the KDE for each spot with counts as uint16.
+    """
+
+def kde_at_coord(
+    counts: GridCounts,
+    genes: list[str],
+    kernel: NDArray[np.float32],
+    coordinates: tuple[NDArray[np.int_], NDArray[np.int_]],
+    *,
+    n_threads: int | None = None,
+) -> _CsxArray:
+    """
+    Calculate KDE at the given coordinates.
+    """
+
+def categorical_coordinate(
+    x: NDArray[np.int32], y: NDArray[np.int32], *, n_threads: int | None = None
+) -> tuple[NDArray[np.int32], NDArray[np.int32]]:
+    """
+    Get the codes and the coordinates (comparable to a pandas.Categorical)
+    """
+
+def coordinate_as_string(
+    x: NDArray[np.int32], y: NDArray[np.int32], *, n_threads: int | None = None
+) -> NDArray[np.str_]:
+    """
+    Concatenate two int arrays elementwise into a string representation (i.e. 'x_y').
+    """
+
+def cosinef32_and_celltypei8(
+    counts: GridCounts,
+    genes: list[str],
+    signatures: NDArray[np.float32],
+    kernel: NDArray[np.float32],
+    *,
+    log: bool = False,
+    chunk_size: tuple[int, int] = (500, 500),
+    n_threads: int | None = None,
+) -> tuple[NDArray[np.float32], NDArray[np.float32], NDArray[np.int8]]:
+    """
+    Calculate the cosine similarity given counts and signatures and assign the most
+    similar celltype.
+    """
+
+def cosinef32_and_celltypei16(
+    counts: GridCounts,
+    genes: list[str],
+    signatures: NDArray[np.float32],
+    kernel: NDArray[np.float32],
+    *,
+    log: bool = False,
+    chunk_size: tuple[int, int] = (500, 500),
+    n_threads: int | None = None,
+) -> tuple[NDArray[np.float32], NDArray[np.float32], NDArray[np.int16]]:
+    """
+    Calculate the cosine similarity given counts and signatures and assign the most
+    similar celltype.
+    """
+
+class GridCounts:
+    """
+    Object holding each gene as count data in a sparse 2D-grid.
+    """
+
+    shape: tuple[int, int]
+    """
+    tuple[int, int]: Shape of the count arrays.
+    """
+
+    def __init__(
+        self,
+        counts: dict[str, _Csx],
+        *,
+        resolution: float | None = None,
+        n_threads: int | None = None,
+    ):
+        """
+        Parameters
+        ----------
+        counts : dict[str, scipy.sparse.csr_array | scipy.sparse.csr_matrix | scipy.sparse.csc_array | scipy.sparse.csc_matrix]
+            Gene counts.
+        resolution : float, optional
+            Resolution as nm / pixel.
+        n_threads : int, optional
+            Number of threads used for reading and processing file. If `None` this will
+            default to the number of logical CPUs.
+
+        Raises
+        ------
+        ValueError
+            If genes in `counts` do not all have the same shape.
+        """
+
+    @classmethod
+    def from_dataframe(
+        cls,
+        df: DataFrame,
+        *,
+        resolution: float | None = None,
+        binsize: float | None = None,
+        n_threads: int | None = None,
+    ):  # -> Self
+        """
+        Initialize from dataframe.
+
+        Transform a :py:class:`polars.DataFrame` that provides a 'gene', 'x', and 'y'
+        column into :py:class:`sainsc.GridCounts`. If a 'count' column exists it will
+        be used as counts else a count of 1 (single molecule) per row will be assumed.
+
+        Parameters
+        ----------
+        df : polars.DataFrame
+            The data to be transformed.
+        binsize : float or None, optional
+            The size to bin the coordinates by. If None coordinates must be integers.
+        resolution : float, optional
+            Resolution of each coordinate unit in nm. The default is 1,000 i.e. measurements
+            are in um.
+        n_threads : int, optional
+            Number of threads used for initializing :py:class:`sainsc.LazyKDE`.
+            If `None` this will default to the number of logical CPUs.
+
+        Returns
+        -------
+        sainsc.GridCounts
+        """
+
+    def as_dataframe(self) -> DataFrame:
+        """
+        Convert to a dataframe with 'gene', 'x', 'y', and 'count' column.
+
+        Returns
+        -------
+        polars.DataFrame
+        """
+
+    def __getitem__(self, key: str) -> _CsxArray: ...
+    def __setitem__(self, key: str, value: _Csx): ...
+    def __delitem__(self, key: str): ...
+    def __len__(self) -> int: ...
+    def __contains__(self, item: str) -> bool: ...
+    def __eq__(self, other) -> bool: ...
+    def __ne__(self, other) -> bool: ...
+    def get(self, key: str, default: _CsxArray | None = None) -> _CsxArray | None:
+        """
+        Get the counts for a gene.
+
+        Parameters
+        ----------
+        key : str
+            Name of the gene to retrieve.
+
+        Returns
+        -------
+        scipy.sparse.csr_array | scipy.sparse.csc_array | None
+        """
+
+    def genes(self) -> list[str]:
+        """
+        Get all available genes.
+
+        Returns
+        -------
+        list[str]
+        """
+
+    def gene_counts(self) -> dict[str, int]:
+        """
+        Number of counts per gene.
+
+        Returns
+        -------
+        dict[str, int]
+            Mapping from gene to number of counts.
+        """
+
+    def grid_counts(self) -> NDArray[np.uintc]:
+        """
+        Counts per pixel.
+
+        Aggregates counts across all genes.
+
+        Returns
+        -------
+        numpy.ndarray[numpy.uintc]
+        """
+
+    def select_genes(self, genes: set[str]):
+        """
+        Keep selected genes.
+
+        Parameters
+        ----------
+        genes : set[str]
+            List of gene names to keep.
+        """
+
+    def filter_genes_by_count(self, min: int = 1, max: int = 4_294_967_295):
+        """
+        Filter genes by minimum and maximum count thresholds.
+
+        Parameters
+        ----------
+        min : int, optional
+            Minimum count threshold.
+        max : int, optional
+            Maximum count threshold.
+        """
+
+    def crop(self, x: tuple[int | None, int | None], y: tuple[int | None, int | None]):
+        """
+        Crop the field of view for all genes.
+
+        Parameters
+        ----------
+        x : tuple[int | None, int | None]
+            Range to crop as `(xmin, xmax)`
+        y : tuple[int | None, int | None]
+            Range to crop as `(ymin, ymax)`
+        """
+
+    def filter_mask(self, mask: NDArray[np.bool_]):
+        """
+        Filter all genes with a binary mask.
+
+        Parameters
+        ----------
+        mask : numpy.ndarray[numpy.bool]
+            All counts where `mask` is `False` will be set to 0.
+        """
+
+    @property
+    def resolution(self) -> float | None:
+        """
+        float | None: Resolution in nm / pixel.
+
+        Raises
+        ------
+            TypeError
+                If setting with a type other than `float` or `int`.
+        """
+
+    @resolution.setter
+    def resolution(self, resolution: float): ...
+    @property
+    def n_threads(self) -> int:
+        """
+        int: Number of threads used for processing.
+
+        Raises
+        ------
+            TypeError
+                If setting with a type other than `int` or less than 0.
+        """
+
+    @n_threads.setter
+    def n_threads(self, n_threads: int): ...