senoquant 1.0.0b2__py3-none-any.whl → 1.0.0b4__py3-none-any.whl

senoquant/tabs/visualization/plots/umap.py

@@ -0,0 +1,140 @@
+"""UMAP plot handler for visualization."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Iterable
+
+from .base import PlotData, SenoQuantPlot
+
+
+class UMAPData(PlotData):
+    """Configuration data for UMAP plot."""
+
+    pass
+
+
+class UMAPPlot(SenoQuantPlot):
+    """UMAP dimensionality reduction plot handler."""
+
+    feature_type = "UMAP"
+    order = 1
+
+    def build(self) -> None:
+        """Build the UI for UMAP plot configuration."""
+        # Minimal UI for now; can add controls for n_components, metric, etc. later
+        pass
+
+    def plot(
+        self, 
+        temp_dir: Path, 
+        input_path: Path, 
+        export_format: str,
+        markers: list[str] | None = None,
+        thresholds: dict[str, float] | None = None,
+    ) -> Iterable[Path]:
+        """Generate UMAP plot from input CSV.
+
+        Parameters
+        ----------
+        temp_dir : Path
+            Temporary directory to write plot output.
+        input_path : Path
+            Path to input CSV file or folder containing CSV files.
+        export_format : str
+            Output format ("png", "svg", or "pdf").
+        markers : list of str, optional
+            List of selected markers to include.
+        thresholds : dict, optional
+            Dictionary of {marker_name: threshold_value} for filtering.
+
+        Returns
+        -------
+        iterable of Path
+            Paths to generated plot files.
+        """
+        try:
+            try:
+                import pandas as pd
+            except ImportError:
+                print("[UMAPPlot] pandas is not installed; skipping plot generation.")
+                return []
+            try:
+                import matplotlib.pyplot as plt
+            except ImportError:
+                print("[UMAPPlot] matplotlib is not installed; skipping plot generation.")
+                return []
+            try:
+                from umap import UMAP as UMAPReducer
+            except ImportError:
+                print("[UMAPPlot] umap-learn is not installed; skipping plot generation.")
+                return []
+
+            print(f"[UMAPPlot] Starting with input_path={input_path}")
+            # Find the first data file (CSV or Excel) in the input folder
+            data_files = list(input_path.glob("*.csv")) + list(input_path.glob("*.xlsx")) + list(input_path.glob("*.xls"))
+            print(f"[UMAPPlot] Found {len(data_files)} data files")
+            if not data_files:
+                print(f"[UMAPPlot] No CSV/Excel files found in {input_path}")
+                return []
+            
+            data_file = data_files[0]
+            print(f"[UMAPPlot] Reading {data_file}")
+            if data_file.suffix.lower() in ('.xlsx', '.xls'):
+                df = pd.read_excel(data_file)
+            else:
+                df = pd.read_csv(data_file)
+            print(f"[UMAPPlot] Loaded dataframe with shape {df.shape}")
+            if df.empty:
+                print(f"[UMAPPlot] DataFrame is empty")
+                return []
+
+            # Apply thresholds if provided
+            if thresholds:
+                for marker, thresh in thresholds.items():
+                    col_name = f"{marker}_mean_intensity"
+                    if col_name in df.columns:
+                        # Clip values below threshold to 0
+                        df.loc[df[col_name] < thresh, col_name] = 0
+
+            # Select numeric columns for UMAP
+            if markers:
+                numeric_cols = [f"{m}_mean_intensity" for m in markers if f"{m}_mean_intensity" in df.columns]
+                print(f"[UMAPPlot] Using {len(numeric_cols)} selected markers for UMAP")
+            else:
+                numeric_cols = df.select_dtypes(include=["number"]).columns
+                print(f"[UMAPPlot] Found {len(numeric_cols)} numeric columns (default)")
+            
+            if len(numeric_cols) < 2:
+                print(f"[UMAPPlot] Need at least 2 numeric columns for UMAP, found {len(numeric_cols)}")
+                return []
+
+            X = df[numeric_cols].values
+
+            # Fit UMAP
+            print(f"[UMAPPlot] Fitting UMAP with {len(X)} samples")
+            reducer = UMAPReducer(n_components=2, random_state=42)
+            embedding = reducer.fit_transform(X)
+            print(f"[UMAPPlot] UMAP embedding created with shape {embedding.shape}")
+
+            # Create plot
+            fig, ax = plt.subplots(figsize=(8, 6))
+            ax.scatter(embedding[:, 0], embedding[:, 1], alpha=0.6, s=20)
+            ax.set_xlabel("UMAP 1")
+            ax.set_ylabel("UMAP 2")
+            ax.set_title("UMAP Plot")
+
+            # Save plot
+            output_file = temp_dir / f"umap_plot.{export_format}"
+            print(f"[UMAPPlot] Saving to {output_file}")
+            fig.savefig(str(output_file), dpi=150, bbox_inches="tight")
+            plt.close(fig)
+            print(f"[UMAPPlot] Plot saved successfully")
+
+            return [output_file]
+
+        except Exception as e:
+            import traceback
+            print(f"[UMAPPlot] ERROR generating UMAP plot: {e}")
+            print(traceback.format_exc())
+            return []

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-1.0.0b4.dist-info/METADATA

@@ -0,0 +1,162 @@
+Metadata-Version: 2.4
+Name: senoquant
+Version: 1.0.0b4
+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: PyWavelets>=1.5
+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
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: umap-learn>=0.5
+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: PyWavelets>=1.5; 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: matplotlib>=3.8; extra == "all"
+Requires-Dist: umap-learn>=0.5; 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-1.0.0b4.dist-info}/RECORD

@@ -1,50 +1,50 @@
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 senoquant/napari.yaml,sha256=2r1EpZcV1B3mLv0z3FwjS8e1T-yIMzoWvNj2SBqmftI,1664
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 senoquant/reader/__init__.py,sha256=3lDuOpQC8TGUdfXdpLrr7MaszOVCqKMYM9YaTdq3DVQ,92
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 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
+senoquant/tabs/segmentation/models/default_3d/model.py,sha256=x8zBcoEXXLMMkS2cYGYnZTnl33n9_OjTHJzRJV3aAeM,21758
 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 +134,38 @@ 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=2uRrhWXT8q_8MySYVDoGQyETq8RDHLua5haCwnXehi4,30262
 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
-senoquant-1.0.0b2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-senoquant-1.0.0b2.dist-info/entry_points.txt,sha256=_HUyyJcDeBQVdUKjY3ZW9fqvHLWFn2mPXS_9KBPIzuU,52
-senoquant-1.0.0b2.dist-info/top_level.txt,sha256=zD3JsHkIEr7T58xOr2E7mnQ7fqeju6swI2kSkKUPfX4,10
-senoquant-1.0.0b2.dist-info/RECORD,,
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+senoquant/tabs/spots/models/rmp/model.py,sha256=pdeYaXbQ1lQK1D_ZUhn0Chf9XSDV4dG2Nn4Jht3v3mI,19181
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{senoquant-1.0.0b2.dist-info → senoquant-1.0.0b4.dist-info}/top_level.txt

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

ufish/__init__.py

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