napari-tmidas 0.3.0__py3-none-any.whl → 0.3.1__py3-none-any.whl

napari_tmidas/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.3.0'
-__version_tuple__ = version_tuple = (0, 3, 0)
+__version__ = version = '0.3.1'
+__version_tuple__ = version_tuple = (0, 3, 1)
 
 __commit_id__ = commit_id = None

napari_tmidas/processing_functions/__init__.py

@@ -41,9 +41,17 @@ def discover_and_load_processing_functions(reload: bool = False) -> List[str]:
                     importlib.import_module(module_fullname)
                 
                 print(f"Loaded processing function module: {module_name}")
-            except ImportError as e:
+            except (ImportError, ValueError) as e:
                 # Log the error but continue with other modules
-                print(f"Failed to import {module_name}: {e}")
+                # ValueError catches NumPy binary incompatibility issues
+                error_msg = str(e)
+                if "numpy.dtype size changed" in error_msg:
+                    print(
+                        f"Failed to import {module_name}: NumPy binary incompatibility. "
+                        "Try: pip install --force-reinstall --no-cache-dir scikit-learn-extra"
+                    )
+                else:
+                    print(f"Failed to import {module_name}: {e}")
 
     # Return the list of registered functions
     return BatchProcessingRegistry.list_functions()

napari_tmidas/processing_functions/cellpose_env_manager.py

@@ -67,6 +67,28 @@ class CellposeEnvironmentManager(BaseEnvironmentManager):
             "Installing Cellpose 4 (Cellpose-SAM) in the dedicated environment..."
         )
 
+        # First, install PyTorch with CUDA 12.x support for sm_120 compatibility
+        # RTX PRO 4000 Blackwell has CUDA capability sm_120, which requires newer PyTorch
+        print("Installing PyTorch with CUDA 12.x support (for sm_120 compatibility)...")
+        try:
+            subprocess.check_call(
+                [
+                    env_python,
+                    "-m",
+                    "pip",
+                    "install",
+                    "torch",
+                    "torchvision",
+                    "torchaudio",
+                    "--index-url",
+                    "https://download.pytorch.org/whl/cu124",
+                ]
+            )
+            print("✓ PyTorch with CUDA 12.4 installed successfully")
+        except subprocess.CalledProcessError as e:
+            print(f"✗ Failed to install PyTorch: {e}")
+            raise
+
         # Install packages one by one with error checking
         packages = ["cellpose", "zarr", "tifffile"]
         for package in packages:

napari_tmidas/processing_functions/intensity_label_filter.py

@@ -52,10 +52,18 @@ except (ImportError, ValueError) as e:
     # ValueError: binary incompatibility (e.g., numpy version mismatch)
     KMedoids = None
     _HAS_KMEDOIDS = False
-    print(
-        f"scikit-learn-extra not available ({type(e).__name__}). "
-        "Install with: pip install scikit-learn-extra"
-    )
+    error_msg = str(e)
+    if "numpy.dtype size changed" in error_msg:
+        print(
+            "scikit-learn-extra has a NumPy binary incompatibility. "
+            "This is typically resolved by reinstalling scikit-learn-extra. "
+            "Run: pip install --force-reinstall --no-cache-dir scikit-learn-extra"
+        )
+    else:
+        print(
+            f"scikit-learn-extra not available ({type(e).__name__}). "
+            "Install with: pip install scikit-learn-extra"
+        )
 
 try:
     import pandas as pd

{napari_tmidas-0.3.0.dist-info → napari_tmidas-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.3.0
+Version: 0.3.1
 Summary: A plugin for batch processing of confocal and whole-slide microscopy images of biological tissues
 Author: Marco Meer
 Author-email: marco.meer@pm.me
@@ -151,11 +151,11 @@ Then find napari-tmidas in the **Plugins** menu. [Watch video tutorials →](htt
 
 ### Core Workflows
 
-- **[Image Conversion](docs/basic_processing.md#file-conversion)** - Multi-format microscopy file conversion
+- **[File Conversion](docs/file_conversion.md)** - Multi-format microscopy file conversion (LIF, ND2, CZI, NDPI, Acquifer)
 - **[Batch Processing](docs/basic_processing.md)** - Label operations, filters, channel splitting
 - **[Quality Control](docs/grid_view_overlay.md)** - Visual QC with grid overlay
 - **[Quantification](docs/regionprops_analysis.md)** - Extract measurements from labels
-- **[Colocalization](docs/advanced_processing.md#colocalization)** - Multi-channel ROI analysis
+- **[Colocalization](docs/advanced_processing.md#colocalization-analysis)** - Multi-channel ROI analysis
 
 ### Advanced Features
 
@@ -163,28 +163,25 @@ Then find napari-tmidas in the **Plugins** menu. [Watch video tutorials →](htt
 - [Advanced Filters](docs/advanced_processing.md) - SciPy/scikit-image filters
 - [Batch Label Inspection](docs/basic_processing.md#label-inspection) - Manual correction workflow
 
-## 💻 Installation Options
+## 💻 Installation
 
-**Recommended (latest features):**
-```bash
-pip install git+https://github.com/MercaderLabAnatomy/napari-tmidas.git
-```
+### Step 1: Install napari
 
-**Stable release:**
 ```bash
-pip install napari-tmidas
+mamba create -y -n napari-tmidas -c conda-forge python=3.11
+mamba activate napari-tmidas
+python -m pip install "napari[all]"
 ```
 
-**With deep learning (optional):**
-```bash
-pip install 'napari-tmidas[deep-learning]'  # Includes SAM2
-pip install 'napari-tmidas[all]'            # Everything
-```
+### Step 2: Install napari-tmidas
 
-**Additional setup for SAM2:**
-```bash
-mamba install -c conda-forge ffmpeg  # Required for video processing
-```
+| Your Needs | Command |
+|----------|---------|
+| **Just process & convert images** | `pip install napari-tmidas` |
+| **Need AI features** (SAM2, Cellpose, Spotiflow, etc.) | `pip install 'napari-tmidas[deep-learning]'` |
+| **Want the latest dev features** | `pip install git+https://github.com/MercaderLabAnatomy/napari-tmidas.git` |
+
+**Recommended for most users:** `pip install 'napari-tmidas[deep-learning]'`
 
 ## 🖼️ Screenshots
 

{napari_tmidas-0.3.0.dist-info → napari_tmidas-0.3.1.dist-info}/RECORD

@@ -10,7 +10,7 @@ napari_tmidas/_registry.py,sha256=yunbEoDe1JZREMab4BeP7wka17IwK1toV5g1imju30c,21
 napari_tmidas/_roi_colocalization.py,sha256=0ZSs7JlJKPhGibnETf6Rj746T3YV4AUgynWmZbmNjHw,92257
 napari_tmidas/_sample_data.py,sha256=khuv1jemz_fCjqNwEKMFf83Ju0EN4S89IKydsUMmUxw,645
 napari_tmidas/_ui_utils.py,sha256=wBmaR-3wdgizb234atsjUU2DElsM5-tf4TIsxGLaHzI,1499
-napari_tmidas/_version.py,sha256=5zTqm8rgXsWYBpB2M3Zw_K1D-aV8wP7NsBLrmMKkrAQ,704
+napari_tmidas/_version.py,sha256=gGLpQUQx-ty9SEy9PYw9OgJWWzJLBnCpfJOfzL7SjlI,704
 napari_tmidas/_widget.py,sha256=Uab5WuJK2fgdlGga6iNnHsiZjRMUq2KM3u0N5JJW8DA,5495
 napari_tmidas/_writer.py,sha256=wbVfHFjjHdybSg37VR4lVmL-kdCkDZsUPDJ66AVLaFQ,1941
 napari_tmidas/napari.yaml,sha256=1Am1dA0-ZtCXk6veIT6jrMz3zwQ7dF8_p9tZTFx_vTg,2641
@@ -37,16 +37,16 @@ napari_tmidas/_tests/test_viscy_virtual_staining.py,sha256=iy7YnM65lQhn01UqEMsF6
 napari_tmidas/_tests/test_widget.py,sha256=0qKDzyfqGnKKY6smqYiruZEWBQjW5fU98ZHeSE5Ei2Q,3263
 napari_tmidas/_tests/test_windows_basic.py,sha256=nELpwQErf5m1mStIns5jZ4l5BD-_J9XG8IP_CrhSGWw,2311
 napari_tmidas/_tests/test_writer.py,sha256=4_MlZM9a5So74J16_4tIOJc6pwTOw9R0-oAE_YioIx4,122
-napari_tmidas/processing_functions/__init__.py,sha256=1yG17a_ddZXXc12uwB-PkwsBeQD7YvpyKHqc8sZAfgc,2325
+napari_tmidas/processing_functions/__init__.py,sha256=wX0zNxzvlUVxfBUbgZmQ-6sNy88UntlwNT8RRIevHC8,2767
 napari_tmidas/processing_functions/basic.py,sha256=3kA7GwCJDkkPyIRMZL5hFDSbz-8jjehMlWsQtjdOlro,44500
 napari_tmidas/processing_functions/careamics_denoising.py,sha256=DFE_6lefeqckAvx-1EqwzJSU3iR3g3ujBGRnF_fnpoM,11638
 napari_tmidas/processing_functions/careamics_env_manager.py,sha256=ca3e4a8s5mMZdgbYLtk21sXDyhIAulgvH1x5k__wDjw,10342
-napari_tmidas/processing_functions/cellpose_env_manager.py,sha256=0HFlHZVbXs2nEead6-VUrHjPhkFkcujP-a0-5Ys_mvA,16718
+napari_tmidas/processing_functions/cellpose_env_manager.py,sha256=vaS3JNMbPu8re68eWgCxs3Hcy1CsrUL7pWgoUtGfIl0,17585
 napari_tmidas/processing_functions/cellpose_segmentation.py,sha256=qChVwyvGL5nqXjeS0pD0XOxgkyojdiHVXghvdMzdpWI,12280
 napari_tmidas/processing_functions/colocalization.py,sha256=_QZu1rI_Mt4lnME0YhaAg0RP9Wjof0smpbJoqXoGXR8,25518
 napari_tmidas/processing_functions/file_compression.py,sha256=mxR-yqBdc-T1XI3StIXpW8h5xGdCOtLQjt8uoRFpDSY,6859
 napari_tmidas/processing_functions/grid_view_overlay.py,sha256=pZ-5CsHx2tvvW_3QCz5d1-UpleHPES9pj40ZhAf4rrQ,22991
-napari_tmidas/processing_functions/intensity_label_filter.py,sha256=cTVCyEPWsPFyz0xdzDj2RwrQaXOzi_kCXUdo2WtwzeY,13887
+napari_tmidas/processing_functions/intensity_label_filter.py,sha256=w2vfSIBa4fZSkL5eM2mSqljJYXguV4zyPQUV--6P_Dw,14240
 napari_tmidas/processing_functions/regionprops_analysis.py,sha256=ySmzlY_F8uXWQIoSXJFge30jkWFg6G8HhjDVbk4v2rU,45828
 napari_tmidas/processing_functions/sam2_env_manager.py,sha256=w-X493XdHWAE8UhyHhEEVJ3uvLi2VdS-UFU7yPqnagg,2569
 napari_tmidas/processing_functions/sam2_mp4.py,sha256=lEdrqQP36_kw2g3soyu81CCRXCkI5DdSExfq5Bc5kig,11523
@@ -58,9 +58,9 @@ napari_tmidas/processing_functions/timepoint_merger.py,sha256=7pXyfcI2rXZz6_TP3v
 napari_tmidas/processing_functions/trackastra_tracking.py,sha256=IkFk5HoEZmKdcu5jXri4WMhHN1KTADDMxSpeYfPgSbo,9976
 napari_tmidas/processing_functions/viscy_env_manager.py,sha256=eJ9NsyrtypvxRAFVir9n9RtKaaj6GTpIrOFNLScoVDY,11999
 napari_tmidas/processing_functions/viscy_virtual_staining.py,sha256=Aa__YweYzSFYUTkbneDZ2lxRBplozrQvXGSiMFzUhA4,12422
-napari_tmidas-0.3.0.dist-info/licenses/LICENSE,sha256=tSjiOqj57exmEIfP2YVPCEeQf0cH49S6HheQR8IiY3g,1485
-napari_tmidas-0.3.0.dist-info/METADATA,sha256=AzkyQb_qivFSaoKhZ2nrdjfIuowz8barUmy6NsnUQ60,10175
-napari_tmidas-0.3.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-napari_tmidas-0.3.0.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
-napari_tmidas-0.3.0.dist-info/top_level.txt,sha256=63ybdxCZ4SeT13f_Ou4TsivGV_2Gtm_pJOXToAt30_E,14
-napari_tmidas-0.3.0.dist-info/RECORD,,
+napari_tmidas-0.3.1.dist-info/licenses/LICENSE,sha256=tSjiOqj57exmEIfP2YVPCEeQf0cH49S6HheQR8IiY3g,1485
+napari_tmidas-0.3.1.dist-info/METADATA,sha256=Ohv8-GQ7y0K40UyIr6YX6l8z3_WbVcxSbTaV0lPvUjE,10348
+napari_tmidas-0.3.1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+napari_tmidas-0.3.1.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
+napari_tmidas-0.3.1.dist-info/top_level.txt,sha256=63ybdxCZ4SeT13f_Ou4TsivGV_2Gtm_pJOXToAt30_E,14
+napari_tmidas-0.3.1.dist-info/RECORD,,