napari-tmidas 0.1.7.1__py3-none-any.whl → 0.1.8.5__py3-none-any.whl

napari_tmidas/processing_functions/colocalization.py

@@ -11,8 +11,6 @@ returns statistics about their colocalization.
 import numpy as np
 from skimage import measure
 
-from napari_tmidas._registry import BatchProcessingRegistry
-
 
 def get_nonzero_labels(image):
     """Get unique, non-zero labels from an image."""
@@ -133,23 +131,23 @@ def process_single_roi(
     return result
 
 
-@BatchProcessingRegistry.register(
-    name="ROI Colocalization",
-    suffix="_coloc",
-    description="Analyze colocalization between ROIs in multiple channel label images",
-    parameters={
-        "get_sizes": {
-            "type": bool,
-            "default": False,
-            "description": "Calculate size statistics",
-        },
-        "size_method": {
-            "type": str,
-            "default": "median",
-            "description": "Method for size calculation (median or sum)",
-        },
-    },
-)
+# @BatchProcessingRegistry.register(
+#     name="ROI Colocalization",
+#     suffix="_coloc",
+#     description="Analyze colocalization between ROIs in multiple channel label images",
+#     parameters={
+#         "get_sizes": {
+#             "type": bool,
+#             "default": False,
+#             "description": "Calculate size statistics",
+#         },
+#         "size_method": {
+#             "type": str,
+#             "default": "median",
+#             "description": "Method for size calculation (median or sum)",
+#         },
+#     },
+# )
 def roi_colocalization(image, get_sizes=False, size_method="median"):
     """
     Calculate colocalization between channels for a multi-channel label image.

napari_tmidas/processing_functions/file_compression.py

@@ -0,0 +1,205 @@
+# processing_functions/file_compression.py
+"""
+Processing functions for compressing files using pzstd.
+
+This module provides a function to compress files using the Zstandard compression algorithm
+via the pzstd tool. It compresses image files after they have been processed by other functions
+in the batch processing pipeline.
+
+Note: This requires the pzstd tool to be installed on the system.
+"""
+import subprocess
+
+import numpy as np
+
+from napari_tmidas._file_selector import ProcessingWorker
+from napari_tmidas._registry import BatchProcessingRegistry
+
+
+def check_pzstd_installed():
+    """Check if pzstd is installed on the system."""
+    try:
+        subprocess.run(["pzstd", "--version"], capture_output=True, text=True)
+        return True
+    except (subprocess.SubprocessError, FileNotFoundError):
+        return False
+
+
+def compress_file(file_path, remove_source=False, compression_level=3):
+    """
+    Compress a file using pzstd.
+
+    Parameters:
+    -----------
+    file_path : str
+        Path to the file to compress
+    remove_source : bool
+        Whether to remove the source file after compression
+    compression_level : int
+        Compression level (1-22)
+
+    Returns:
+    --------
+    tuple
+        (success, compressed_file_path)
+    """
+    compressed_file = f"{file_path}.zst"
+    command = ["pzstd", "--quiet"]
+
+    # Set compression level
+    if compression_level >= 20:
+        command.extend(["--ultra", f"-{compression_level}"])
+    else:
+        command.append(f"-{compression_level}")
+
+    # Remove source if requested
+    if remove_source:
+        command.append("--rm")
+
+    command.append(file_path)
+
+    try:
+        result = subprocess.run(command, capture_output=True, text=True)
+        return result.returncode == 0, compressed_file
+    except (subprocess.SubprocessError, FileNotFoundError):
+        return False, None
+
+
+@BatchProcessingRegistry.register(
+    name="Compress with Zstandard",
+    suffix="_compressed",
+    description="Compress the processed image file using Zstandard (requires pzstd to be installed)",
+    parameters={
+        "remove_source": {
+            "type": bool,
+            "default": False,
+            "description": "Remove the source file after compression",
+        },
+        "compression_level": {
+            "type": int,
+            "default": 3,
+            "min": 1,
+            "max": 22,
+            "description": "Compression level (1-22, higher = better compression but slower)",
+        },
+    },
+)
+def compress_with_zstandard(
+    image: np.ndarray, remove_source: bool = False, compression_level: int = 3
+) -> np.ndarray:
+    """
+    Process an image and compress the output file using Zstandard.
+
+    This function:
+    1. Takes an image array as input
+    2. Returns the original image unchanged (compression happens to the saved file)
+    3. The batch processing system saves the file
+    4. This function then compresses the saved file using pzstd
+
+    Parameters:
+    -----------
+    image : numpy.ndarray
+        Input image array
+    remove_source : bool
+        Whether to remove the source file after compression (default: False)
+    compression_level : int
+        Compression level (1-22) (default: 3)
+
+    Returns:
+    --------
+    numpy.ndarray
+        The original image (unchanged)
+    """
+    # Check if pzstd is installed
+    if not check_pzstd_installed():
+        print("Warning: pzstd is not installed. Compression will be skipped.")
+        return image
+
+    # Instead of trying to modify the array, set attributes on the processing function itself
+    compress_with_zstandard.compress_after_save = True
+    compress_with_zstandard.remove_source = remove_source
+    compress_with_zstandard.compression_level = compression_level
+
+    # Return the image unchanged - compression happens after saving
+    return image
+
+
+# Monkey patch the batch processing system to compress files after saving
+# This is a bit of a hack, but it allows us to compress files after they've been saved
+# by the batch processing system
+
+# Store the original save_file function
+
+
+original_process_file = ProcessingWorker.process_file
+
+
+# Replace it with our modified version that compresses after saving
+def process_file_with_compression(self, filepath):
+    """Modified process_file function that compresses files after saving."""
+    result = original_process_file(self, filepath)
+
+    # Check if there's a result and if we should compress it
+    if isinstance(result, dict):
+        # Single output file
+        if "processed_file" in result:
+            output_path = result["processed_file"]
+            # Check if the processed image had compression metadata
+            if (
+                hasattr(self.processing_func, "compress_after_save")
+                and self.processing_func.compress_after_save
+            ):
+                # Get compression parameters
+                remove_source = getattr(
+                    self.processing_func, "remove_source", False
+                )
+                compression_level = getattr(
+                    self.processing_func, "compression_level", 3
+                )
+
+                # Compress the file
+                success, compressed_path = compress_file(
+                    output_path, remove_source, compression_level
+                )
+
+                if success:
+                    # Update the result with the compressed file path
+                    result["processed_file"] = compressed_path
+
+        # Multiple output files
+        elif "processed_files" in result:
+            output_paths = result["processed_files"]
+            # Check if the processed image had compression metadata
+            if (
+                hasattr(self.processing_func, "compress_after_save")
+                and self.processing_func.compress_after_save
+            ):
+                # Get compression parameters
+                remove_source = getattr(
+                    self.processing_func, "remove_source", False
+                )
+                compression_level = getattr(
+                    self.processing_func, "compression_level", 3
+                )
+
+                # Compress each file
+                compressed_paths = []
+                for output_path in output_paths:
+                    success, compressed_path = compress_file(
+                        output_path, remove_source, compression_level
+                    )
+
+                    if success:
+                        compressed_paths.append(compressed_path)
+                    else:
+                        compressed_paths.append(output_path)
+
+                # Update the result with the compressed file paths
+                result["processed_files"] = compressed_paths
+
+    return result
+
+
+# Apply the monkey patch if pzstd is available
+if check_pzstd_installed():
+    ProcessingWorker.process_file = process_file_with_compression

napari_tmidas/processing_functions/skimage_filters.py

@@ -39,7 +39,7 @@ if SKIMAGE_AVAILABLE:
     @BatchProcessingRegistry.register(
         name="Otsu Thresholding (semantic)",
         suffix="_otsu_semantic",
-        description="Threshold image using Otsu's method",
+        description="Threshold image using Otsu's method to obtain a binary image",
     )
     def otsu_thresholding(image: np.ndarray) -> np.ndarray:
         """
@@ -54,7 +54,7 @@ if SKIMAGE_AVAILABLE:
     @BatchProcessingRegistry.register(
         name="Otsu Thresholding (instance)",
         suffix="_otsu_labels",
-        description="Threshold image using Otsu's method",
+        description="Threshold image using Otsu's method to obtain a multi-label image",
     )
     def otsu_thresholding_instance(image: np.ndarray) -> np.ndarray:
         """
@@ -68,7 +68,7 @@ if SKIMAGE_AVAILABLE:
     @BatchProcessingRegistry.register(
         name="Manual Thresholding (8-bit)",
         suffix="_thresh",
-        description="Threshold image using a fixed threshold",
+        description="Threshold image using a fixed threshold to obtain a binary image",
         parameters={
             "threshold": {
                 "type": int,
@@ -91,9 +91,9 @@ if SKIMAGE_AVAILABLE:
 
     # remove small objects
     @BatchProcessingRegistry.register(
-        name="Remove Small Objects",
+        name="Remove Small Labels",
         suffix="_rm_small",
-        description="Remove small objects from the binary image",
+        description="Remove small labels from label images",
         parameters={
             "min_size": {
                 "type": int,
@@ -108,8 +108,27 @@ if SKIMAGE_AVAILABLE:
         image: np.ndarray, min_size: int = 100
     ) -> np.ndarray:
         """
-        Remove small objects from the binary image
+        Remove small labels from label images
         """
         return skimage.morphology.remove_small_objects(
             image, min_size=min_size
         )
+
+
+# binary to labels
+@BatchProcessingRegistry.register(
+    name="Binary to Labels",
+    suffix="_labels",
+    description="Convert binary images to label images (connected components)",
+)
+def binary_to_labels(image: np.ndarray) -> np.ndarray:
+    """
+    Convert binary images to label images (connected components)
+    """
+    # Make a copy of the input image to avoid modifying the original
+    label_image = image.copy()
+
+    # Convert binary image to label image using connected components
+    label_image = skimage.measure.label(label_image, connectivity=2)
+
+    return label_image

{napari_tmidas-0.1.7.1.dist-info → napari_tmidas-0.1.8.5.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.1.7.1
-Summary: Tissue Microscopy Image Data Analysis Suite
+Version: 0.1.8.5
+Summary: A plugin for batch processing of confocal microscopy images
 Author: Marco Meer
 Author-email: marco.meer@pm.me
 License: 
@@ -58,6 +58,14 @@ Requires-Dist: magicgui
 Requires-Dist: qtpy
 Requires-Dist: scikit-image
 Requires-Dist: pyqt5
+Requires-Dist: tqdm
+Requires-Dist: scikit-image
+Requires-Dist: ome-zarr
+Requires-Dist: napari-ome-zarr
+Requires-Dist: torch
+Requires-Dist: torchvision
+Requires-Dist: timm
+Requires-Dist: opencv-python
 Provides-Extra: testing
 Requires-Dist: tox; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -80,7 +88,15 @@ The `napari-tmidas` plugin consists of a growing collection of pipelines for fas
 ## Feature Overview
 
 1. **Image Processing**
-   - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
+   - Process image folders with:
+     - Gamma correction & histogram equalization
+     - Z-projection and channel splitting
+     - Gaussian & median filters
+     - Thresholding (Otsu/manual)
+     - Label cleaning & binary conversion
+     - RGB to labels conversion
+     - Cellpose 3.0 automated segmentation
+     - File compression (Zstandard)
 
 2. **Label Inspection**
    - Review and edit label images with auto-save
@@ -112,19 +128,27 @@ Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
-To install the latest development version:
+It is recommended to install the latest development version:
 
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
 ### Dependencies
-To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats and to write ome-zarr:
 
-    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari ome-zarr napari-ome-zarr
+To use the Batch Microscopy Image Conversion pipeline, we need some libraries to read microscopy formats:
+
+    pip install nd2 readlif tiffslide pylibCZIrw acquifer-napari
 
 For the Batch Crop Anything pipeline, we need to install MobileSAM and its dependencies:
 
     pip install git+https://github.com/ChaoningZhang/MobileSAM.git
-    pip install torch torchvision timm opencv-python
+
+
+If you want to batch compress images using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
+
+    sudo apt-get install zstd    # for Linux
+    brew install zstd            # for macOS
+    choco install zstandard      # for Windows
+
 
 ## Usage
 
@@ -169,9 +193,9 @@ If you have already segmented a folder full of images and now you want to maybe
 ![image](https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e)
 
 ### Crop Anything
-This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`
+This pipeline combines the Segment Anything Model (SAM) for automatic object detection with an interactive interface for selecting and cropping multiple objects from images. To launch the widget, open `Plugins > T-MIDAS > Batch Crop Anything`. Click the image below to see a video demo.
 
-![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
+[![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)](https://youtu.be/xPh0dRD_FbE)
 
 ### ROI Colocalization
 This pipeline quantifies colocalization between labeled regions of interest (ROIs) across multiple image channels. It determines the extent of overlap between ROIs in a reference channel and those in one or two other channels. The output is a table of colocalization counts. Optionally, the size of reference channel ROIs, as well as the total or median size of colocalizing ROIs in the other channels, can be included. Colocalization is determined using Boolean masking. The number of colocalizing instances is determined by counting unique label IDs within the overlapping regions. Typically, the reference channel contains larger structures, while other channels contain smaller, potentially nested, structures. For example, the reference channel might contain cell bodies, with the second and third channels containing nuclei and sub-nuclear objects, respectively.

{napari_tmidas-0.1.7.1.dist-info → napari_tmidas-0.1.8.5.dist-info}/RECORD

@@ -1,13 +1,13 @@
 napari_tmidas/__init__.py,sha256=YNBLESwk8jr_TlDdkSC1CwH0tf0CKHF1i2_efzLjdpk,589
-napari_tmidas/_crop_anything.py,sha256=UxC0FbktgBPvxNMJtpXEATzIk0UFUO1DqRfrKy7bf30,39982
-napari_tmidas/_file_conversion.py,sha256=RnEOVavzApkeJfYb0_TmH6KWca0kpgxHZ517E65OQVI,71398
-napari_tmidas/_file_selector.py,sha256=8Plkoofa9nG5hSyOpQd6qjZlc8sFgBErnTwT5C24stg,34993
+napari_tmidas/_crop_anything.py,sha256=NItpE6uzfeKujh8a53TDDkFN2thpKC5NGiXMpAmSnnM,45446
+napari_tmidas/_file_conversion.py,sha256=V6evJmggUwOFzJO203Y5ltboHXEWNJQckZPedGRkrLI,72203
+napari_tmidas/_file_selector.py,sha256=sZOY0QNwyAgugsEzG5pqZLfrVeCHwjPEW2C_BHndzyI,39595
 napari_tmidas/_label_inspection.py,sha256=hCxKE0zYk-qBh4ohqiZcEGLXa-3lL8p88y45p2WnE1g,7329
 napari_tmidas/_reader.py,sha256=A9_hdDxtVkVGmbOsbqgnARCSvpEh7GGPo7ylzmbnu8o,2485
 napari_tmidas/_registry.py,sha256=Oz9HFJh41MKRLeKxRuc7x7yzc-OrmoTdRFnfngFU_XE,2007
 napari_tmidas/_roi_colocalization.py,sha256=OVjdHvtFN07DgrtTX8uqbrxZL6jVwl2L3klorgW2C9k,43196
 napari_tmidas/_sample_data.py,sha256=khuv1jemz_fCjqNwEKMFf83Ju0EN4S89IKydsUMmUxw,645
-napari_tmidas/_version.py,sha256=p8f2-ePBt5y3pqs0DIoraU1Kr2laBz6Syt-saDgpANc,516
+napari_tmidas/_version.py,sha256=c4rCUXy1zrstQ6YUlnpyulFDT5n9rZNVdxW9dQYyGe0,516
 napari_tmidas/_widget.py,sha256=u9uf9WILAwZg_InhFyjWInY4ej1TV1a59dR8Fe3vNF8,4794
 napari_tmidas/_writer.py,sha256=wbVfHFjjHdybSg37VR4lVmL-kdCkDZsUPDJ66AVLaFQ,1941
 napari_tmidas/napari.yaml,sha256=1Am1dA0-ZtCXk6veIT6jrMz3zwQ7dF8_p9tZTFx_vTg,2641
@@ -17,13 +17,16 @@ napari_tmidas/_tests/test_sample_data.py,sha256=D1HU_C3hWpO3mlSW_7Z94xaYHDtxz0XU
 napari_tmidas/_tests/test_widget.py,sha256=I_d-Cra_CTcS0QdMItg_HMphvhj0XCx81JnFyCHk9lg,2204
 napari_tmidas/_tests/test_writer.py,sha256=4_MlZM9a5So74J16_4tIOJc6pwTOw9R0-oAE_YioIx4,122
 napari_tmidas/processing_functions/__init__.py,sha256=osXY9jSgDsrwFaS6ShPHP0wGRxMuX1mHRN9EDa9l41g,1891
-napari_tmidas/processing_functions/basic.py,sha256=5v-_nRQK1Dssu8f3LFJIW73urmTEm3BX8lf9lrb9BBM,3690
-napari_tmidas/processing_functions/colocalization.py,sha256=O0-gJFVq62lfpOWNu0bJVYKZcsO6Z3HG6FsFkYho_j4,7684
+napari_tmidas/processing_functions/basic.py,sha256=TJFvJ9AfUp7MBseUAgryLJXdqj0gSLSKqlEPxE3s1n0,6694
+napari_tmidas/processing_functions/cellpose_env_manager.py,sha256=zngS5eborsJUimFn_g1Lm_YOZk2ZNIKxceWNxOjpxEg,4885
+napari_tmidas/processing_functions/cellpose_segmentation.py,sha256=7BCHj_QA1QJEl1NrsuoIFAJ040_SCWw0U-U_xjCyk18,16187
+napari_tmidas/processing_functions/colocalization.py,sha256=AiTTVAcVhKuuHZhrj5IHwbzns7-GE6ewvFqhYy1L-do,7657
+napari_tmidas/processing_functions/file_compression.py,sha256=mxR-yqBdc-T1XI3StIXpW8h5xGdCOtLQjt8uoRFpDSY,6859
 napari_tmidas/processing_functions/scipy_filters.py,sha256=kKpDAlQQ0ZNbkt77QUWi-Bwolk6MMDvtG_bZJV3MjOo,1612
-napari_tmidas/processing_functions/skimage_filters.py,sha256=kOwdYVUUqIYz9h-EBrYu0sFsmKkmqoTegkDoDywFwmE,3373
-napari_tmidas-0.1.7.1.dist-info/licenses/LICENSE,sha256=tSjiOqj57exmEIfP2YVPCEeQf0cH49S6HheQR8IiY3g,1485
-napari_tmidas-0.1.7.1.dist-info/METADATA,sha256=424PwkL2y7N3lM35qYZFGgyds3kAaT0Jq6tFwkeQbvA,11118
-napari_tmidas-0.1.7.1.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-napari_tmidas-0.1.7.1.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
-napari_tmidas-0.1.7.1.dist-info/top_level.txt,sha256=63ybdxCZ4SeT13f_Ou4TsivGV_2Gtm_pJOXToAt30_E,14
-napari_tmidas-0.1.7.1.dist-info/RECORD,,
+napari_tmidas/processing_functions/skimage_filters.py,sha256=6wSROKH71zwSFBOZ22zgp-4Nrq79GNd7znOitiH3Z3c,4030
+napari_tmidas-0.1.8.5.dist-info/licenses/LICENSE,sha256=tSjiOqj57exmEIfP2YVPCEeQf0cH49S6HheQR8IiY3g,1485
+napari_tmidas-0.1.8.5.dist-info/METADATA,sha256=bo5HfzWOBpQME6b-kkw7wkg71oQUjbU2hhN2D9lWwbA,11812
+napari_tmidas-0.1.8.5.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
+napari_tmidas-0.1.8.5.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
+napari_tmidas-0.1.8.5.dist-info/top_level.txt,sha256=63ybdxCZ4SeT13f_Ou4TsivGV_2Gtm_pJOXToAt30_E,14
+napari_tmidas-0.1.8.5.dist-info/RECORD,,

{napari_tmidas-0.1.7.1.dist-info → napari_tmidas-0.1.8.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (79.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any