napari-tmidas 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

napari_tmidas/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.3'
-__version_tuple__ = version_tuple = (0, 1, 3)
+__version__ = version = '0.1.4'
+__version_tuple__ = version_tuple = (0, 1, 4)

napari_tmidas/napari.yaml

@@ -24,6 +24,9 @@ contributions:
     - id: napari-tmidas.file_selector
       python_name: napari_tmidas._file_selector:napari_experimental_provide_dock_widget
       title: File selector
+    - id: napari-tmidas._file_conversion
+      python_name: napari_tmidas._file_conversion:napari_experimental_provide_dock_widget
+      title: File converter
   readers:
     - command: napari-tmidas.get_reader
       accepts_directories: false
@@ -44,3 +47,5 @@ contributions:
       display_name: File selector
     - command: napari-tmidas._label_inspection
       display_name: Label inspector
+    - command: napari-tmidas._file_conversion
+      display_name: File converter

napari_tmidas/processing_functions/basic.py

@@ -8,53 +8,35 @@ from napari_tmidas._registry import BatchProcessingRegistry
 
 
 @BatchProcessingRegistry.register(
-    name="Min-Max Normalization",
-    suffix="_normalized",
-    description="Normalize image values to range [0, 1] using min-max scaling",
-)
-def normalize_image(image: np.ndarray) -> np.ndarray:
-    """
-    Simple min-max normalization
-    """
-    if image.min() == image.max():
-        return np.zeros_like(image, dtype=float)
-    return (image - image.min()) / (image.max() - image.min())
-
-
-@BatchProcessingRegistry.register(
-    name="Contrast Stretch",
-    suffix="_contrast",
-    description="Stretch the contrast by clipping percentiles and rescaling",
+    name="Gamma Correction",
+    suffix="_gamma",
+    description="Apply gamma correction to the image (>1: enhance bright regions, <1: enhance dark regions)",
     parameters={
-        "low_percentile": {
-            "type": float,
-            "default": 2.0,
-            "min": 0.0,
-            "max": 49.0,
-            "description": "Low percentile to clip",
-        },
-        "high_percentile": {
+        "gamma": {
             "type": float,
-            "default": 98.0,
-            "min": 51.0,
-            "max": 100.0,
-            "description": "High percentile to clip",
+            "default": 1.0,
+            "min": 0.1,
+            "max": 10.0,
+            "description": "Gamma correction factor",
         },
     },
 )
-def contrast_stretch(
-    image: np.ndarray,
-    low_percentile: float = 2.0,
-    high_percentile: float = 98.0,
-) -> np.ndarray:
+def gamma_correction(image: np.ndarray, gamma: float = 1.0) -> np.ndarray:
     """
-    Stretch contrast by clipping percentiles
+    Apply gamma correction to the image
     """
-    p_low = np.percentile(image, low_percentile)
-    p_high = np.percentile(image, high_percentile)
+    # Determine maximum value based on dtype
+    max_val = (
+        np.iinfo(image.dtype).max
+        if np.issubdtype(image.dtype, np.integer)
+        else 1.0
+    )
+
+    # Normalize image to [0, 1]
+    normalized = image.astype(np.float32) / max_val
+
+    # Apply gamma correction
+    corrected = np.power(normalized, gamma)
 
-    # Clip and normalize
-    image_clipped = np.clip(image, p_low, p_high)
-    if p_high == p_low:
-        return np.zeros_like(image, dtype=float)
-    return (image_clipped - p_low) / (p_high - p_low)
+    # Scale back to original range and dtype
+    return (corrected * max_val).clip(0, max_val).astype(image.dtype)

napari_tmidas/processing_functions/skimage_filters.py

@@ -7,6 +7,7 @@ import numpy as np
 try:
     import skimage.exposure
     import skimage.filters
+    import skimage.morphology
 
     SKIMAGE_AVAILABLE = True
 except ImportError:
@@ -19,49 +20,38 @@ from napari_tmidas._registry import BatchProcessingRegistry
 
 if SKIMAGE_AVAILABLE:
 
-    @BatchProcessingRegistry.register(
-        name="Adaptive Histogram Equalization",
-        suffix="_clahe",
-        description="Enhance contrast using Contrast Limited Adaptive Histogram Equalization",
-        parameters={
-            "kernel_size": {
-                "type": int,
-                "default": 8,
-                "min": 4,
-                "max": 64,
-                "description": "Size of local region for histogram equalization",
-            },
-            "clip_limit": {
-                "type": float,
-                "default": 0.01,
-                "min": 0.001,
-                "max": 0.1,
-                "description": "Clipping limit for contrast enhancement",
-            },
-        },
-    )
-    def adaptive_hist_eq(
-        image: np.ndarray, kernel_size: int = 8, clip_limit: float = 0.01
-    ) -> np.ndarray:
-        """
-        Apply Contrast Limited Adaptive Histogram Equalization
-        """
-        # CLAHE expects image in [0, 1] range
-        img_norm = skimage.exposure.rescale_intensity(image, out_range=(0, 1))
-        return skimage.exposure.equalize_adapthist(
-            img_norm, kernel_size=kernel_size, clip_limit=clip_limit
-        )
-
-    @BatchProcessingRegistry.register(
-        name="Edge Detection",
-        suffix="_edges",
-        description="Detect edges using Sobel filter",
-    )
-    def edge_detection(image: np.ndarray) -> np.ndarray:
-        """
-        Detect edges using Sobel filter
-        """
-        return skimage.filters.sobel(image)
+    # @BatchProcessingRegistry.register(
+    #     name="Adaptive Histogram Equalization",
+    #     suffix="_clahe",
+    #     description="Enhance contrast using Contrast Limited Adaptive Histogram Equalization",
+    #     parameters={
+    #         "kernel_size": {
+    #             "type": int,
+    #             "default": 8,
+    #             "min": 4,
+    #             "max": 64,
+    #             "description": "Size of local region for histogram equalization",
+    #         },
+    #         "clip_limit": {
+    #             "type": float,
+    #             "default": 0.01,
+    #             "min": 0.001,
+    #             "max": 0.1,
+    #             "description": "Clipping limit for contrast enhancement",
+    #         },
+    #     },
+    # )
+    # def adaptive_hist_eq(
+    #     image: np.ndarray, kernel_size: int = 8, clip_limit: float = 0.01
+    # ) -> np.ndarray:
+    #     """
+    #     Apply Contrast Limited Adaptive Histogram Equalization
+    #     """
+    #     # CLAHE expects image in [0, 1] range
+    #     img_norm = skimage.exposure.rescale_intensity(image, out_range=(0, 1))
+    #     return skimage.exposure.equalize_adapthist(
+    #         img_norm, kernel_size=kernel_size, clip_limit=clip_limit
+    #     )
 
     # simple otsu thresholding
     @BatchProcessingRegistry.register(
@@ -110,4 +100,31 @@ if SKIMAGE_AVAILABLE:
         """
         Threshold image using a fixed threshold
         """
+        # convert to 8-bit
+        image = skimage.img_as_ubyte(image)
         return image > threshold
+
+    # remove small objects
+    @BatchProcessingRegistry.register(
+        name="Remove Small Objects",
+        suffix="_rm_small",
+        description="Remove small objects from the binary image",
+        parameters={
+            "min_size": {
+                "type": int,
+                "default": 100,
+                "min": 1,
+                "max": 100000,
+                "description": "Remove labels smaller than: ",
+            },
+        },
+    )
+    def remove_small_objects(
+        image: np.ndarray, min_size: int = 100
+    ) -> np.ndarray:
+        """
+        Remove small objects from the binary image
+        """
+        return skimage.morphology.remove_small_objects(
+            image, min_size=min_size
+        )

{napari_tmidas-0.1.3.dist-info → napari_tmidas-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: napari-tmidas
-Version: 0.1.3
+Version: 0.1.4
 Summary: Tissue Microscopy Image Data Analysis Suite
 Author: Marco Meer
 Author-email: marco.meer@pm.me
@@ -79,10 +79,13 @@ The Tissue Microscopy Image Data Analysis Suite (short: T-MIDAS), is a collectio
 
 ## Installation
 
-First install Napari in a virtual environment following the latest [Napari installation instructions](https://github.com/Napari/napari?tab=readme-ov-file#installation).
+First install Napari in a virtual environment:
 
+    mamba create -y -n napari-tmidas -c conda-forge python=3.11
+    mamba activate napari-tmidas
+    python -m pip install "napari[all]"
 
-After you have activated the environment, you can install `napari-tmidas` via [pip]:
+Now you can install `napari-tmidas` via [pip]:
 
     pip install napari-tmidas
 
@@ -90,31 +93,46 @@ To install the latest development version:
 
     pip install git+https://github.com/macromeer/napari-tmidas.git
 
+### Dependencies
+For the File converter, we need some libraries to read some microscopy formats and to write ome-zarr:
+
+    pip install nd2 readlif tiffslide pylibCZIrw ome-zarr
+
+
 ## Usage
 
 You can find the installed plugin here:
-   
+
 ![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
 
+
+### File converter
+
+You might first want to batch convert microscopy image data. Currently, this plugin supports `.nd2, .lif, .ndpi, .czi`. After launching the file converter, you can scan a folder of your choice for microscopy image data. It will also detect series images that you can preview. Start by selecting an original image in the first column of the table. This allows you to preview or convert.
+
+![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
+
+
+
 ### File inspector
 
 1. After opening `Plugins > T-MIDAS > File selector`, enter the path to the folder containing the images to be processed (currently supports TIF, later also ZARR). You can also filter for filename suffix.
-   
+
 ![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
 
 2. As a result, a table appears with the found images.
-   
+
 ![image](https://github.com/user-attachments/assets/8360942a-be8f-49ec-bc25-385ee43bd601)
 
 3. Next, select a processing function, set parameters if applicable and `Start Batch Processing`.
-   
+
 ![image](https://github.com/user-attachments/assets/05929660-6672-4f76-89da-4f17749ccfad)
 
-4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay. 
-    
+4. You can click on the images in the table to show them in the viewer. For example first click on one of the `Original Files`, and then the corresponding `Processed File` to see an overlay.
+
 ![image](https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce)
 
-Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect. 
+Note that whenever you click on an `Original File` or `Processed File` in the table, it will replace the one that is currently shown in the viewer. So naturally, you'd first select the original image, and then the processed image to correctly see the image pair that you want to inspect.
 
 ### Label inspector
 If you have already segmented a folder full of images and now you want to maybe inspect and edit each label image, you can use the `Plugins > T-MIDAS > Label inspector`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
@@ -122,6 +140,7 @@ 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)
 
 
+
 ## Contributing
 
 Contributions are very welcome. Tests can be run with [tox], please ensure

{napari_tmidas-0.1.3.dist-info → napari_tmidas-0.1.4.dist-info}/RECORD

@@ -1,25 +1,26 @@
 napari_tmidas/__init__.py,sha256=Z9mznblUlUsRyH3d4k8SxUo4iXLMwJXURbq41QzhPpo,459
-napari_tmidas/_file_selector.py,sha256=YzjS-XIqLD8826n50KXAc0GfQeXOhvDs41QP3-bTtCU,17471
-napari_tmidas/_label_inspection.py,sha256=0icowMfyNRnaxgTIOi8KHxLXKfpfqtShIl8iVR4wJjc,4819
+napari_tmidas/_file_conversion.py,sha256=jkoP3x-4iePkdGfv3_5XQnXNpHhn9dxLlRCB98yVAJs,54395
+napari_tmidas/_file_selector.py,sha256=XLbqeQ4fG86gLHgmPZzrcmMTir5gpneO32KumJY8ZbM,27369
+napari_tmidas/_label_inspection.py,sha256=5p0heCX1xCQVYDGHe_R2gPwbZpl6sXIqLBwqbZLJKqo,6983
 napari_tmidas/_reader.py,sha256=A9_hdDxtVkVGmbOsbqgnARCSvpEh7GGPo7ylzmbnu8o,2485
 napari_tmidas/_registry.py,sha256=Oz9HFJh41MKRLeKxRuc7x7yzc-OrmoTdRFnfngFU_XE,2007
 napari_tmidas/_sample_data.py,sha256=khuv1jemz_fCjqNwEKMFf83Ju0EN4S89IKydsUMmUxw,645
-napari_tmidas/_version.py,sha256=NIzzV8ZM0W-CSLuEs1weG4zPrn_-8yr1AwwI1iuS6yo,511
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 napari_tmidas/_widget.py,sha256=u9uf9WILAwZg_InhFyjWInY4ej1TV1a59dR8Fe3vNF8,4794
 napari_tmidas/_writer.py,sha256=wbVfHFjjHdybSg37VR4lVmL-kdCkDZsUPDJ66AVLaFQ,1941
-napari_tmidas/napari.yaml,sha256=Xmui3_7pxNxOkIFRWsZWuka56d6PXLQ2rl4XvMDl2aw,1839
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 napari_tmidas/_tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 napari_tmidas/_tests/test_reader.py,sha256=gN_2StATLZYUL56X27ImJTVru_qSoFiY4vtgajcx3H0,975
 napari_tmidas/_tests/test_sample_data.py,sha256=D1HU_C3hWpO3mlSW_7Z94xaYHDtxz0XUrMjQoYop9Ag,104
 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=g7tQ25UIxA26n6GBYcHlkSjUbv_lD-7x_Sd-ZvWbzUY,1711
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 napari_tmidas/processing_functions/scipy_filters.py,sha256=kKpDAlQQ0ZNbkt77QUWi-Bwolk6MMDvtG_bZJV3MjOo,1612
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-napari_tmidas-0.1.3.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
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