senoquant 1.0.0b2__py3-none-any.whl → 1.0.0b3__py3-none-any.whl

senoquant/tabs/spots/ufish_utils/core.py

@@ -0,0 +1,357 @@
+"""UFish-based spot enhancement utilities.
+
+This module wraps UFish inference for SenoQuant spot detection workflows.
+It handles:
+
+- optional import of UFish from site-packages or vendored sources,
+- ONNX Runtime execution-provider selection,
+- model/weights caching between calls, and
+- default ONNX weight retrieval from the SenoQuant Hugging Face model repo.
+
+Notes
+-----
+Weight loading priority is:
+
+1. explicit ``UFishConfig.weights_path``,
+2. legacy ``UFishConfig.load_from_internet``, then
+3. default ``ufish.onnx`` resolved via :func:`ensure_hf_model`.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+import sys
+from types import MethodType
+from typing import TYPE_CHECKING, Any, cast
+
+import numpy as np
+
+from senoquant.tabs.segmentation.models.hf import (
+    DEFAULT_REPO_ID,
+    ensure_hf_model,
+)
+
+try:  # pragma: no cover - optional dependency
+    from ufish.api import UFish
+except ImportError:  # pragma: no cover - optional dependency
+    _repo_root = Path(__file__).resolve().parents[5]
+    _vendored_root = _repo_root / "_vendor" / "ufish"
+    if _vendored_root.exists():
+        vendored_root = str(_vendored_root)
+        if vendored_root not in sys.path:
+            sys.path.insert(0, vendored_root)
+        try:
+            from ufish.api import UFish
+        except ImportError:
+            UFish = None
+    else:
+        UFish = None
+
+try:  # pragma: no cover - optional dependency
+    import onnxruntime as ort
+except ImportError:  # pragma: no cover - optional dependency
+    ort = None
+
+if TYPE_CHECKING:  # pragma: no cover - typing only
+    from ufish.api import UFish as UFishType
+
+
+@dataclass(slots=True)
+class UFishConfig:
+    """Configuration for UFish enhancement.
+
+    Parameters
+    ----------
+    weights_path : str or None, optional
+        Explicit local path to ONNX/PyTorch weights. When provided, this path
+        is used directly and takes precedence over all other loading modes.
+    load_from_internet : bool, optional
+        Legacy compatibility mode that calls
+        ``UFish.load_weights_from_internet()`` directly.
+    device : {"cuda", "dml", "mps"} or None, optional
+        Preferred accelerator mode used to influence ONNX Runtime provider
+        ordering when constructing UFish sessions.
+    """
+
+    weights_path: str | None = None
+    load_from_internet: bool = False
+    device: str | None = None
+
+
+class _UFishState:
+    """In-process cache for the UFish model and loaded weights."""
+
+    def __init__(self) -> None:
+        """Initialize empty cached state."""
+        self.model: UFishType | None = None
+        self.weights_loaded = False
+        self.device: str | None = None
+        self.weights_path: str | None = None
+
+
+_UFISH_STATE = _UFishState()
+_UFISH_HF_FILENAME = "ufish.onnx"
+
+
+def _ensure_ufish_available() -> None:
+    """Raise a helpful error when UFish cannot be imported.
+
+    Raises
+    ------
+    ImportError
+        If the ``ufish`` package is unavailable from both normal and vendored
+        import locations.
+    """
+    if UFish is None:  # pragma: no cover - import guard
+        msg = "ufish is required for spot enhancement."
+        raise ImportError(msg)
+
+
+def _resolve_default_weights_path() -> Path:
+    """Resolve the default UFish ONNX path.
+
+    Returns
+    -------
+    pathlib.Path
+        Local path to ``ufish.onnx``. The file is downloaded to the
+        ``ufish_utils`` directory if it does not already exist.
+
+    Raises
+    ------
+    RuntimeError
+        If the Hugging Face download helper is unavailable or download fails.
+    """
+    target_dir = Path(__file__).resolve().parent
+    return ensure_hf_model(
+        _UFISH_HF_FILENAME,
+        target_dir,
+        repo_id=DEFAULT_REPO_ID,
+    )
+
+
+def _preferred_providers() -> list[str]:
+    """Return ONNX Runtime providers ordered by GPU preference.
+
+    Returns
+    -------
+    list[str]
+        Providers available in the current runtime, ordered from most
+        preferred accelerator to CPU fallback.
+    """
+    if ort is None:
+        return []
+    available = set(ort.get_available_providers())
+    preferred = [
+        "CUDAExecutionProvider",
+        "ROCMExecutionProvider",
+        "DmlExecutionProvider",
+        "DirectMLExecutionProvider",
+        "CoreMLExecutionProvider",
+        "CPUExecutionProvider",
+    ]
+    providers = [provider for provider in preferred if provider in available]
+    return providers or list(available)
+
+
+def _select_onnx_providers(device: str | None) -> list[str]:
+    """Choose execution providers for a requested device hint.
+
+    Parameters
+    ----------
+    device : str or None
+        Device hint from :class:`UFishConfig`.
+
+    Returns
+    -------
+    list[str]
+        Provider names to pass to ``onnxruntime.InferenceSession``.
+    """
+    preferred = _preferred_providers()
+    if not device:
+        return preferred
+    if device == "cuda":
+        return [
+            p
+            for p in preferred
+            if p in {"CUDAExecutionProvider", "CPUExecutionProvider"}
+        ]
+    if device == "dml":
+        return [
+            p
+            for p in preferred
+            if p
+            in {
+                "DmlExecutionProvider",
+                "DirectMLExecutionProvider",
+                "CPUExecutionProvider",
+            }
+        ]
+    if device == "mps":
+        return [
+            p
+            for p in preferred
+            if p in {"CoreMLExecutionProvider", "CPUExecutionProvider"}
+        ]
+    return preferred
+
+
+def _patch_onnx_loader(model: UFishType) -> None:
+    """Monkey-patch UFish ONNX loader to use SenoQuant provider selection.
+
+    Parameters
+    ----------
+    model : UFishType
+        UFish instance whose private ``_load_onnx`` method will be replaced.
+    """
+    if ort is None:
+        return
+    ort_any = cast("Any", ort)
+
+    def _load_onnx(
+        self: UFishType,
+        onnx_path: str,
+        providers: list[str] | None = None,
+    ) -> None:
+        providers = providers or _select_onnx_providers(
+            getattr(self, "_device", None),
+        )
+        self.ort_session = ort_any.InferenceSession(
+            str(onnx_path),
+            providers=providers,
+        )
+        self.model = None
+
+    model._load_onnx = MethodType(_load_onnx, model)  # noqa: SLF001
+
+
+def _get_ufish(config: UFishConfig) -> UFishType:
+    """Return a cached UFish instance for the requested configuration.
+
+    Parameters
+    ----------
+    config : UFishConfig
+        Runtime configuration used to determine whether the cached model can be
+        reused or must be re-instantiated.
+
+    Returns
+    -------
+    UFishType
+        Ready-to-use UFish instance with patched ONNX loading behavior.
+    """
+    _ensure_ufish_available()
+    if _UFISH_STATE.model is None or _UFISH_STATE.device != config.device:
+        ufish_cls = cast("type[UFishType]", UFish)
+        ufish_any = cast("Any", ufish_cls)
+        if config.device:
+            _UFISH_STATE.model = ufish_any(device=config.device)
+        else:
+            _UFISH_STATE.model = ufish_any()
+        _patch_onnx_loader(cast("UFishType", _UFISH_STATE.model))
+        _UFISH_STATE.weights_loaded = False
+        _UFISH_STATE.device = config.device
+        _UFISH_STATE.weights_path = None
+    return cast("UFishType", _UFISH_STATE.model)
+
+
+def _ensure_weights(model: UFishType, config: UFishConfig) -> None:
+    """Ensure model weights are loaded according to configuration.
+
+    Parameters
+    ----------
+    model : UFishType
+        Active UFish model instance.
+    config : UFishConfig
+        Weight source and device settings.
+
+    Raises
+    ------
+    RuntimeError
+        If neither Hugging Face/default loading nor fallback loading succeeds.
+    """
+    if config.weights_path:
+        weights_path = Path(config.weights_path).expanduser().resolve()
+        resolved_path = str(weights_path)
+        if _UFISH_STATE.weights_loaded and _UFISH_STATE.weights_path == resolved_path:
+            return
+        model.load_weights(resolved_path)
+        _UFISH_STATE.weights_loaded = True
+        _UFISH_STATE.weights_path = resolved_path
+        return
+
+    if config.load_from_internet:
+        if _UFISH_STATE.weights_loaded and _UFISH_STATE.weights_path == "internet":
+            return
+        model.load_weights_from_internet()
+        _UFISH_STATE.weights_loaded = True
+        _UFISH_STATE.weights_path = "internet"
+        return
+
+    try:
+        weights_path = _resolve_default_weights_path()
+    except RuntimeError:
+        # Keep legacy behavior when HF download dependencies are unavailable.
+        if _UFISH_STATE.weights_loaded and _UFISH_STATE.weights_path == "default":
+            return
+        model.load_weights()
+        _UFISH_STATE.weights_loaded = True
+        _UFISH_STATE.weights_path = "default"
+        return
+    except Exception as exc:
+        try:
+            if _UFISH_STATE.weights_loaded and _UFISH_STATE.weights_path == "default":
+                return
+            model.load_weights()
+            _UFISH_STATE.weights_loaded = True
+            _UFISH_STATE.weights_path = "default"
+            return
+        except Exception:
+            msg = (
+                "Could not load UFish weights from local default or Hugging Face. "
+                "Provide UFishConfig(weights_path=...) or ensure model download access."
+            )
+            raise RuntimeError(msg) from exc
+
+    resolved_path = str(weights_path)
+    if _UFISH_STATE.weights_loaded and _UFISH_STATE.weights_path == resolved_path:
+        return
+    model.load_weights(resolved_path)
+    _UFISH_STATE.weights_loaded = True
+    _UFISH_STATE.weights_path = resolved_path
+
+
+def enhance_image(
+    image: np.ndarray,
+    *,
+    config: UFishConfig | None = None,
+) -> np.ndarray:
+    """Enhance an image using UFish.
+
+    Parameters
+    ----------
+    image : numpy.ndarray
+        Input image array. UFish supports 2D images and common 3D stack
+        layouts handled by UFish internally.
+    config : UFishConfig or None, optional
+        Optional runtime configuration. If omitted, default behavior is used.
+
+    Returns
+    -------
+    numpy.ndarray
+        Enhanced image produced by UFish with the same dimensionality as the
+        input image.
+
+    Raises
+    ------
+    ImportError
+        If UFish cannot be imported.
+    RuntimeError
+        If weights cannot be loaded from configured/default sources.
+    """
+    if config is None:
+        config = UFishConfig()
+    model = _get_ufish(config)
+    _ensure_weights(model, config)
+    image = np.asarray(image)
+    _pred_spots, enhanced = model.predict(image)
+    return np.asarray(enhanced)

senoquant/utils.py

@@ -11,7 +11,7 @@ def layer_data_asarray(layer, *, squeeze: bool = True) -> np.ndarray:
     Parameters
     ----------
     layer : object
-        Napari layer instance providing a ``data`` attribute.
+        napari layer instance providing a ``data`` attribute.
     squeeze : bool, optional
         Whether to remove singleton dimensions.
 

senoquant-1.0.0b3.dist-info/METADATA

@@ -0,0 +1,161 @@
+Metadata-Version: 2.4
+Name: senoquant
+Version: 1.0.0b3
+Summary: napari plugin for spatial quantification of senescence markers in tissue imaging
+Author: SenoQuant Contributors
+Maintainer: SenoQuant Contributors
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/HaamsRee/senoquant
+Project-URL: Documentation, https://haamsree.github.io/senoquant/
+Project-URL: Repository, https://github.com/HaamsRee/senoquant
+Project-URL: Bug Tracker, https://github.com/HaamsRee/senoquant/issues
+Keywords: napari,plugin,senescence,quantification,microscopy,image analysis,segmentation,spot detection
+Classifier: Development Status :: 4 - Beta
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: bioio>=3.2.0
+Requires-Dist: bioio-czi>=2.4.2
+Requires-Dist: bioio-dv>=1.2.0
+Requires-Dist: bioio-imageio>=1.3.0
+Requires-Dist: bioio-lif>=1.4.0
+Requires-Dist: bioio-nd2>=1.6.0
+Requires-Dist: bioio-ome-tiff>=1.4.0
+Requires-Dist: bioio-ome-zarr>=3.2.1
+Requires-Dist: bioio-sldy>=1.4.0
+Requires-Dist: bioio-tifffile>=1.3.0
+Requires-Dist: bioio-tiff-glob>=1.2.0
+Requires-Dist: numpy<=1.26.4,>=1.23
+Requires-Dist: pandas>=2.0
+Requires-Dist: cellpose==4.0.8
+Requires-Dist: onnx>=1.16
+Requires-Dist: onnxruntime>=1.21.0; platform_system == "Darwin"
+Requires-Dist: onnxruntime-gpu>=1.21.0; platform_system != "Darwin"
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: huggingface_hub>=0.23.0
+Requires-Dist: scikit-image<0.25,>=0.22
+Requires-Dist: scipy>=1.8
+Requires-Dist: senoquant-stardist-ext>=0.1.1
+Requires-Dist: dask[array]>=2024.4
+Requires-Dist: dask[distributed]>=2024.4
+Provides-Extra: gpu
+Requires-Dist: cupy-cuda12x>=12.0; extra == "gpu"
+Requires-Dist: cucim>=23.4; extra == "gpu"
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Requires-Dist: bioio>=3.2.0; extra == "all"
+Requires-Dist: bioio-czi>=2.4.2; extra == "all"
+Requires-Dist: bioio-dv>=1.2.0; extra == "all"
+Requires-Dist: bioio-imageio>=1.3.0; extra == "all"
+Requires-Dist: bioio-lif>=1.4.0; extra == "all"
+Requires-Dist: bioio-nd2>=1.6.0; extra == "all"
+Requires-Dist: bioio-ome-tiff>=1.4.0; extra == "all"
+Requires-Dist: bioio-ome-zarr>=3.2.1; extra == "all"
+Requires-Dist: bioio-sldy>=1.4.0; extra == "all"
+Requires-Dist: bioio-tifffile>=1.3.0; extra == "all"
+Requires-Dist: bioio-tiff-glob>=1.2.0; extra == "all"
+Requires-Dist: numpy<=1.26.4,>=1.23; extra == "all"
+Requires-Dist: pandas>=2.0; extra == "all"
+Requires-Dist: cellpose==4.0.8; extra == "all"
+Requires-Dist: onnx>=1.16; extra == "all"
+Requires-Dist: onnxruntime>=1.21.0; platform_system == "Darwin" and extra == "all"
+Requires-Dist: onnxruntime-gpu>=1.21.0; platform_system != "Darwin" and extra == "all"
+Requires-Dist: openpyxl>=3.1; extra == "all"
+Requires-Dist: huggingface_hub>=0.23.0; extra == "all"
+Requires-Dist: scikit-image<0.25,>=0.22; extra == "all"
+Requires-Dist: scipy>=1.8; extra == "all"
+Requires-Dist: senoquant-stardist-ext>=0.1.1; extra == "all"
+Requires-Dist: dask[array]>=2024.4; extra == "all"
+Requires-Dist: dask[distributed]>=2024.4; extra == "all"
+Requires-Dist: cupy-cuda12x>=12.0; extra == "all"
+Requires-Dist: cucim>=23.4; extra == "all"
+Dynamic: license-file
+
+# SenoQuant
+
+![tests](https://github.com/HaamsRee/senoquant/actions/workflows/tests.yml/badge.svg)
+[![PyPI version](https://badge.fury.io/py/senoquant.svg)](https://badge.fury.io/py/senoquant)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+
+SenoQuant is a versatile [napari](https://napari.org/stable/index.html) plugin designed for comprehensive, accurate,
+and unbiased spatial quantification and prediction of senescence markers
+across diverse tissue contexts.
+
+## Features
+
+- Segment nuclei and cytoplasm with built-in models, including StarDist ONNX, Cellpose SAM, and morphology-based models.
+- Detect punctate spots with a U-FISH-based detector.
+- Quantify marker intensity, morphology, spot counts, and spot colocalization.
+- Run batch workflows across folders, including profile save/load and multi-scene support.
+- Read microscopy formats via BioIO, including OME-TIFF, ND2, LIF, CZI, Zarr, and more.
+- *Upcoming*: Integrate custom models for predicting senescence markers.
+
+## Installation
+
+### Installer (recommended)
+
+#### Windows
+
+Download the Windows installer (`.exe`) from the [latest release](https://github.com/HaamsRee/senoquant/releases/latest).
+
+#### macOS
+
+Download the macOS installer (`.pkg`) from the [latest release](https://github.com/HaamsRee/senoquant/releases/latest).
+
+#### Linux
+
+Installer support for Linux is under construction.
+
+### Manual installation
+
+For conda/pip/uv setup, see the [developer installation guide](https://haamsree.github.io/senoquant/developer/installation/).
+
+## Quick start
+
+Use the documentation workflow for the most up-to-date instructions.
+
+- Start with the [installation guide](https://haamsree.github.io/senoquant/user/installation/).
+- Follow the [quick start guide](https://haamsree.github.io/senoquant/user/quickstart/).
+- Then use tab-specific guides for [segmentation](https://haamsree.github.io/senoquant/user/segmentation/), [spots](https://haamsree.github.io/senoquant/user/spots/), [quantification](https://haamsree.github.io/senoquant/user/quantification/), and [batch](https://haamsree.github.io/senoquant/user/batch/).
+
+## Documentation
+
+Full documentation is available at [https://haamsree.github.io/senoquant/](https://haamsree.github.io/senoquant/).
+
+- [Installation guide](https://haamsree.github.io/senoquant/user/installation/).
+- [Quick start tutorial](https://haamsree.github.io/senoquant/user/quickstart/).
+- [Segmentation models](https://haamsree.github.io/senoquant/user/segmentation/).
+- [Spot detection](https://haamsree.github.io/senoquant/user/spots/).
+- [Quantification features](https://haamsree.github.io/senoquant/user/quantification/).
+- [Batch processing](https://haamsree.github.io/senoquant/user/batch/).
+- [API reference](https://haamsree.github.io/senoquant/api/).
+
+## Development
+
+See the [contributing guide](https://haamsree.github.io/senoquant/developer/contributing/) for development setup instructions.
+
+## How to cite
+
+If you use SenoQuant in your research, please cite it using the metadata in `CITATION.cff`.
+
+On GitHub, open the repository page and click `Cite this repository` in the right sidebar to copy a formatted citation.
+
+## Acknowledgements
+
+SenoQuant builds on and integrates excellent open-source projects.
+
+- [napari](https://napari.org/).
+- [StarDist](https://github.com/stardist/stardist).
+- [Cellpose](https://github.com/MouseLand/cellpose).
+- [U-FISH](https://github.com/UFISH-Team/U-FISH).
+- [BioIO](https://github.com/bioio-devs/bioio).

{senoquant-1.0.0b2.dist-info → senoquant-1.0.0b3.dist-info}/RECORD

@@ -1,50 +1,50 @@
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+senoquant/__init__.py,sha256=mNRYmhG-SXPlokw7tiuHYRGLzqtfECSRH-QIpZiEJbk,269
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 senoquant/_widget.py,sha256=nuNaKvWAx7aKXORAipOUf7sUI5I3DvZazXnwrJcBqcw,1102
 senoquant/napari.yaml,sha256=2r1EpZcV1B3mLv0z3FwjS8e1T-yIMzoWvNj2SBqmftI,1664
-senoquant/utils.py,sha256=JAE1S_UUkrcNrEg2JKDB33VPqt4UWOFtH45hY5uPrbo,641
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 senoquant/reader/__init__.py,sha256=3lDuOpQC8TGUdfXdpLrr7MaszOVCqKMYM9YaTdq3DVQ,92
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 senoquant/tabs/__init__.py,sha256=DnIT3E7XRSw2CmlZ-Ma4aYpoUFSFjF-66kMDNPaZEmU,371
 senoquant/tabs/batch/__init__.py,sha256=0-xDYyAEEch9Yq7OhGeTkgoXus52Y_SQjqvtIbI-I20,291
-senoquant/tabs/batch/backend.py,sha256=rFjpObFsnF4rpYxrcrctE7UGy9qSah_V1v1AlyL4KSw,24166
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 senoquant/tabs/batch/config.py,sha256=w6DR0Nw6BL0hrFacQPIAHb-wCirYnogYJgmAPy2j9zo,8639
-senoquant/tabs/batch/frontend.py,sha256=dFubaU1uvqRCKMAyx2owyTPERjkiRIrfXBkdZvujgUw,51811
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 senoquant/tabs/batch/io.py,sha256=mggktbDDsGr4hQvpu4oj1eJcxG-xiPwfquO7QBesdDk,8382
 senoquant/tabs/batch/layers.py,sha256=JjWS6WVZ3YOd-KZ4AjqstRF0qTPwOxOgGHd5FXrer08,2078
 senoquant/tabs/quantification/__init__.py,sha256=iCqW7cg9QFfUdnYF7JSwOEus_tm66IZXdxSShy7RxwA,34
 senoquant/tabs/quantification/backend.py,sha256=uEHV-JNEXddj5jptKDSrz6Lnt3MIYTzmBu0aV0vjLDY,7337
-senoquant/tabs/quantification/frontend.py,sha256=HKMlkzUf5b8_N9OA5Ki6J5hW02JouBgr4IGtI6AUulQ,29068
+senoquant/tabs/quantification/frontend.py,sha256=veDnWxwyVkXt60fdq85Nrv8XZJTowNxX5mpxaMO8qQA,29068
 senoquant/tabs/quantification/features/__init__.py,sha256=XR8nPIAGuVpDT8bqWH0qaI-GeZGp9JOKUD7F77dOd7s,2076
 senoquant/tabs/quantification/features/base.py,sha256=OIH_qwKYyKbTwXGhjQzgwNzoabMURActvmA-gUEoU_8,4018
 senoquant/tabs/quantification/features/roi.py,sha256=wLvFJJ1a2W5x4BOUDrLvou_rje1KmDzUp5nwQvzooTU,11397
 senoquant/tabs/quantification/features/marker/__init__.py,sha256=8twYCiUtoau-6rfcLCVndyKkaG1i9v9fGo6IfQ_Eyuo,98
 senoquant/tabs/quantification/features/marker/config.py,sha256=H0n4xY8ZFSVDIKmsDnQZr_nW0zPpL4PLyKMCtYOrprE,1793
-senoquant/tabs/quantification/features/marker/dialog.py,sha256=pnQVzt2RGSjAQ6oqswr2WY7sMk0skMSsLOj55hXFBw0,14886
-senoquant/tabs/quantification/features/marker/export.py,sha256=Tbk-TvK2cLCg-x8YH4F2jNXEXW2jOJ8-4-PqvZGJGXA,27210
+senoquant/tabs/quantification/features/marker/dialog.py,sha256=89q5OjHAPG8wjoPKtdNLuFYRDAzLR1ysGJrxhcAJ7wU,15616
+senoquant/tabs/quantification/features/marker/export.py,sha256=SNChfDTyr3rTwLmEs2sfYkLZ_EbdqTofKgbZeUyhJbI,29874
 senoquant/tabs/quantification/features/marker/feature.py,sha256=cWZqUm_KTR-vdQpVXK5FiHKCdMlSkJJ8IJjV3bhLUpM,3917
 senoquant/tabs/quantification/features/marker/morphology.py,sha256=eIwhZgTIoPXtJOUHLR9GJ4okaSCVBoJ3NFSzTQycZiI,8676
-senoquant/tabs/quantification/features/marker/rows.py,sha256=Uycekb1O5g7YXggUusgsL6rhJNJhT7IjEZUbKM6LcWI,23528
+senoquant/tabs/quantification/features/marker/rows.py,sha256=PyvXVRodq3DjPuRj1o4IlqMzZh-N8bRT8Dy_fXiWjJQ,23528
 senoquant/tabs/quantification/features/marker/thresholding.py,sha256=jwyc_G774NgmWXElI29Z8j4cX0A8CPqs4PtsobCHCxc,1213
 senoquant/tabs/quantification/features/spots/__init__.py,sha256=XpfiHRHNCmCeaBWuTZsyy_qybswkYYVS_Y4oY885xe0,95
 senoquant/tabs/quantification/features/spots/config.py,sha256=wLSnDvYFWZRN7_D2ih4aCugSlTtNaC5CW3NzGKYoyCM,1616
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 senoquant/tabs/quantification/features/spots/feature.py,sha256=8Zk-SbJDA-Ge9kx46oEisacVVrCJL3cb7LA_zivqWkw,3896
 senoquant/tabs/quantification/features/spots/morphology.py,sha256=toK9exTD3CDX3vEKFN2CcT14f-03ASTJxSpQv8ZfC1M,8498
 senoquant/tabs/quantification/features/spots/rows.py,sha256=9FPrWmNLN6MPeVKpi3knPakkwJ8kR0b4sW0WIMLgaoM,7291
 senoquant/tabs/segmentation/__init__.py,sha256=YKSbKlgW372MFEA7xxY3_CUUkXfKX6VSwdoHh_btIaU,32
 senoquant/tabs/segmentation/backend.py,sha256=9DCVEUEFG0zdl0c_IXa7vAiwLCZetkfGJVK_zdrXsIQ,4295
-senoquant/tabs/segmentation/frontend.py,sha256=CVvCbbErVaOG5y-Ds4Ot9y2_0YDYAiCH0-TOtmy-GtI,36560
+senoquant/tabs/segmentation/frontend.py,sha256=8hJeyC9h-sjWso25A5SOIgaut0khXljI1uN2HpFOEq0,37987
 senoquant/tabs/segmentation/models/__init__.py,sha256=0_Jxlyc6wGeOoCPhLxKtcfWa8MqFhFm4-_3ca0zDhME,138
 senoquant/tabs/segmentation/models/base.py,sha256=ND518fqg0XuBNT2AWdlf796LEx8xOX9Jq2Ofcf-MsDY,4335
 senoquant/tabs/segmentation/models/hf.py,sha256=Ns9o3slFSq7Ipyj3u1KrJbJ9zKxykh8A6kjxkzH1A58,1845
 senoquant/tabs/segmentation/models/cpsam/details.json,sha256=A_obIZzrnSLw_JPCPX5wq2ZtqYuo0QE6Ctn_BpgwBC4,1239
-senoquant/tabs/segmentation/models/cpsam/model.py,sha256=U-NiFbci3xLx0e1OKcEq_AYtGAOY0_E-YTrJxvLPFAo,5175
+senoquant/tabs/segmentation/models/cpsam/model.py,sha256=-Y4sqVH67LEj0A8C16aeDhj8KU5BUUbb75QYXRRg23I,5175
 senoquant/tabs/segmentation/models/default_2d/details.json,sha256=S5H14Fk2_dmQNI2_TsXyB6j8PxspmjWC7tNh23VnG80,1338
-senoquant/tabs/segmentation/models/default_2d/model.py,sha256=naNlaFMksND0iSjs2Q-sL-E49eIgsOL1LJxImiy1JA0,23619
+senoquant/tabs/segmentation/models/default_2d/model.py,sha256=LzGyo_X3flZHjprHM4i5qkAry-dJJ-OXwD6l8w6az6Q,21647
 senoquant/tabs/segmentation/models/default_3d/details.json,sha256=a-5YI9Po-IYTG9qHylPd4MMm7ydkRZj2s3EV9sxwGLY,1348
-senoquant/tabs/segmentation/models/default_3d/model.py,sha256=oeJzb5G5Mgox1s8ddglxS6CVCQgVxLzj0E03pxeZ-mI,24196
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 senoquant/tabs/segmentation/models/nuclear_dilation/__init__.py,sha256=5rgBUSDK5ZoD6tKVSzF0OUtF2bbBA29HMffJ_CjPJkA,43
 senoquant/tabs/segmentation/models/nuclear_dilation/details.json,sha256=Vx3XY7PvgrM3EMwhRDeFTr9i7GdWohzO2If1eJ-oQoU,510
 senoquant/tabs/segmentation/models/nuclear_dilation/model.py,sha256=onLX1R9U-n0s3Dc64jmBbYBuyTRvems3czclgbqHAP4,3048
@@ -112,13 +112,14 @@ senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/scripts/__init__.py,sh
 senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/scripts/predict2d.py,sha256=h2eywW4LQZJTaktncG0LOuWr9DdR344O8aOzM6_RTqw,3442
 senoquant/tabs/segmentation/stardist_onnx_utils/_stardist/scripts/predict3d.py,sha256=rpdnoA5XPDjRQ-imu1GO4unbfaO5w8PlFLqd_5lAjvY,3581
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/__init__.py,sha256=uyQVHS-vUdONhvI1CDR718AmWPzMXPl9-6F0bL7sFBU,1430
+senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/stardist_libs.py,sha256=caM1arDjZE4vfJVp61AkH2vqbrXUHssHHcTcL7eKu1I,5788
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/convert/__init__.py,sha256=uimduhVV20E3qfJHjSXZlztQfODxdXm5hO4O7dnbsJc,349
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/convert/cli.py,sha256=l4u5YhqO_aYVm-uNxfTUrndhmphBXvPDR7hCxTk2nYE,1356
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/convert/core.py,sha256=eRx2psv-jjBa5LThNZgxSEI9UjhRtyyWdxDutg3elQE,9038
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/__init__.py,sha256=bYIgnsxd_5Ek9XS5sHWuA5WMIpMpoQshId95FWPUm2I,438
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/cli.py,sha256=WlpZOHVqENkpUWMLHnH6AkmW5U6BAOQJaY0Nqlka_tQ,1082
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/divisibility.py,sha256=OwOpWxui47XI3J1xZTEJdu6El7qqqMSLDeEdIZTTMds,7212
-senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/probe.py,sha256=gf-y55GBI50n94UkCGijH9kVa-OZgeOAs5KwXVvLE9g,3220
+senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/probe.py,sha256=9iDqCc_XAXXS9LQyT3vucCTB9TjnJcOpMssNKIHUFos,3219
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/receptive_field.py,sha256=XfwzLZaKX16Y6ybvUggRpsrXcWdFOHUpORhnD694r7Q,6213
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/rf_cli.py,sha256=mZ5TkHSWWEM8WKNQ-I7qVAOmS0mQ81n7CmsjzBejJzY,1325
 senoquant/tabs/segmentation/stardist_onnx_utils/onnx_framework/inspect/valid_sizes.py,sha256=Zec8DPn5EWgXwuiQ0Tw907Y-kxlRCTx5YUgRpbyevGI,7913
@@ -133,16 +134,28 @@ senoquant/tabs/settings/backend.py,sha256=ZVtmrUYNsox7DiVMlcS666XRyLG7GksgC818oo
 senoquant/tabs/settings/frontend.py,sha256=_hTWJHZeEtU6n6qke31R6Es63knKeHhWZYUZj0ep79s,721
 senoquant/tabs/spots/__init__.py,sha256=dYrAIzX3A5w4TOLRRadxL2agOte_Z0ennuEIOCbJD5w,25
 senoquant/tabs/spots/backend.py,sha256=LZdkNzw-bpK0NClbeLttpg4C_8AqnIFg1W4NaxepTSs,4547
-senoquant/tabs/spots/frontend.py,sha256=34rq06tOw1gBcuc6NGzM73QWvKbwLUxKLAAifruUGOY,26816
+senoquant/tabs/spots/frontend.py,sha256=IGyT-rWbX_vVgaIiDkxkijt6EoAPdnkW2dKOvL2Ziwg,28151
 senoquant/tabs/spots/models/__init__.py,sha256=OKnBIi-aaBsuXmwQNeg4EKeV66gSscedXyZ1-O3cJhY,123
 senoquant/tabs/spots/models/base.py,sha256=VABmb2E7xvWOW8J60ZZkog0ZEG4XyW96qeXJMZVuKT8,2786
-senoquant/tabs/spots/models/rmp/details.json,sha256=ocSkURk8jrwZQidQhU6cwcpPukErmpq1RwLkyGn4-Nc,1243
-senoquant/tabs/spots/models/rmp/model.py,sha256=VwJluYX5NlF4crMsKfzncE9c5cPzX8c9x1l3xi7_pP4,17022
-senoquant/tabs/spots/models/udwt/details.json,sha256=wlZLTFdDFC2JD9Za5D-4fgIAbnZGRO6bSnV2j0pz9nE,2209
-senoquant/tabs/spots/models/udwt/model.py,sha256=Erg-HeFbz773rVyP28I8CAZ1UhbqNWpA4XwQhtWVjJU,14046
-senoquant-1.0.0b2.dist-info/licenses/LICENSE,sha256=wJjNEZJA6A7m6ozqNeq3tXi4X5gzbEGraFm2jw5ahG0,1509
-senoquant-1.0.0b2.dist-info/METADATA,sha256=SaAvLT9BIRXBWOGrb_VE8eBS5oH2twOmFgCWxvdT1AI,7279
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-senoquant-1.0.0b2.dist-info/top_level.txt,sha256=zD3JsHkIEr7T58xOr2E7mnQ7fqeju6swI2kSkKUPfX4,10
-senoquant-1.0.0b2.dist-info/RECORD,,
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{senoquant-1.0.0b2.dist-info → senoquant-1.0.0b3.dist-info}/top_level.txt

@@ -1 +1,2 @@
 senoquant
+ufish

ufish/__init__.py

@@ -0,0 +1 @@
+__version__ = '0.1.1'