napari-tmidas 0.1.7__py3-none-any.whl → 0.1.7.1__py3-none-any.whl

napari_tmidas/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.7'
-__version_tuple__ = version_tuple = (0, 1, 7)
+__version__ = version = '0.1.7.1'
+__version_tuple__ = version_tuple = (0, 1, 7, 1)

{napari_tmidas-0.1.7.dist-info → napari_tmidas-0.1.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-tmidas
-Version: 0.1.7
+Version: 0.1.7.1
 Summary: Tissue Microscopy Image Data Analysis Suite
 Author: Marco Meer
 Author-email: marco.meer@pm.me
@@ -79,20 +79,19 @@ The `napari-tmidas` plugin consists of a growing collection of pipelines for fas
 
 ## Feature Overview
 
-### Current Pipelines
-1. **Batch Image Processing**
+1. **Image Processing**
    - Process image folders with: Gamma correction, Z-projection, channel splitting, Gaussian/median filters, thresholding (Otsu/manual), and label cleaning
 
-2. **Batch Label Inspection**
+2. **Label Inspection**
    - Review and edit label images with auto-save
 
-3. **Batch Microscopy Image Conversion**
+3. **Microscopy Image Conversion**
    - Convert .nd2/.lif/.ndpi/.czi/acquifer → .tif/.zarr with metadata preservation
 
-4. **Batch Crop Anything**
+4. **Crop Anything**
    - Interactive ROI selection via click interface
 
-5. Batch ROI Colocalization
+5. **ROI Colocalization**
    - Count colocalized labels across multiple channels
 
 
@@ -138,13 +137,13 @@ You can find the installed plugin here:
 ![image](https://github.com/user-attachments/assets/504db09a-d66e-49eb-90cd-3237024d9d7a)
 
 
-### Batch Microscopy Image Conversion
+### Microscopy Image Conversion
 
 You can start this pipeline via `Plugins > T-MIDAS > Batch Microscopy Image Conversion`. Currently, this pipeline supports the conversion of `.nd2, .lif, .ndpi, .czi` and acquifer data. After scanning a folder of your choice for microscopy image data, select a file in the first column of the table and preview and export any image data it contains.
 
 ![image](https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b)
 
-### Batch File Processing
+### Image Processing
 
 1. After opening `Plugins > T-MIDAS > Batch Image Processing`, 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.
 
@@ -169,11 +168,16 @@ 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)
 
-### Batch Crop Anything
+### 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`
 
 ![image](https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443)
 
+### 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_coloc_pipeline](https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7)
+
 
 ## Contributing
 

{napari_tmidas-0.1.7.dist-info → napari_tmidas-0.1.7.1.dist-info}/RECORD

@@ -7,7 +7,7 @@ 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=W_EoL8cAL4KhujvbYWEpb9NqRLbbrH0T024lJvRRWHI,511
+napari_tmidas/_version.py,sha256=p8f2-ePBt5y3pqs0DIoraU1Kr2laBz6Syt-saDgpANc,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
@@ -21,9 +21,9 @@ napari_tmidas/processing_functions/basic.py,sha256=5v-_nRQK1Dssu8f3LFJIW73urmTEm
 napari_tmidas/processing_functions/colocalization.py,sha256=O0-gJFVq62lfpOWNu0bJVYKZcsO6Z3HG6FsFkYho_j4,7684
 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.dist-info/licenses/LICENSE,sha256=tSjiOqj57exmEIfP2YVPCEeQf0cH49S6HheQR8IiY3g,1485
-napari_tmidas-0.1.7.dist-info/METADATA,sha256=I9BacR_RRXFooM5PqbTaLb-zwf8OEfw9DJkM974s59I,10174
-napari_tmidas-0.1.7.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-napari_tmidas-0.1.7.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
-napari_tmidas-0.1.7.dist-info/top_level.txt,sha256=63ybdxCZ4SeT13f_Ou4TsivGV_2Gtm_pJOXToAt30_E,14
-napari_tmidas-0.1.7.dist-info/RECORD,,
+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,,