napari-tmidas 0.2.5__py3-none-any.whl → 0.3.0__py3-none-any.whl

{napari_tmidas-0.2.5.dist-info → napari_tmidas-0.3.0.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=9wrJ_4Dlc0arUzKiaIqvTY85rMJma3eb1nNlF3uHAxU,704
+napari_tmidas/_version.py,sha256=5zTqm8rgXsWYBpB2M3Zw_K1D-aV8wP7NsBLrmMKkrAQ,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
@@ -19,13 +19,13 @@ napari_tmidas/_tests/test_env_manager.py,sha256=IQDhdGBRV_YJrYAK6U8cXbDZyvmG9YNW
 napari_tmidas/_tests/test_file_selector.py,sha256=Sbu0BCXTaQAeUJLtOVjIC87AUARbi8J0bXBlMJe53ew,2687
 napari_tmidas/_tests/test_grid_view_overlay.py,sha256=11-l7qqA6Tfi5Pf1VKRTPDg3dG61zrZPxG2SV3mM0Rg,6367
 napari_tmidas/_tests/test_init.py,sha256=xGic9AQn-VtEOloUWIrH1P6_KvJp61nILk35Y09FHTA,3424
-napari_tmidas/_tests/test_intensity_label_filter.py,sha256=PB2aWx48A4qpJ52uR0wIdE9LaFwRKdNwpOVfkiguB0s,7694
+napari_tmidas/_tests/test_intensity_label_filter.py,sha256=ANBg2m9_WZfEKaV0umH1bvYimYSEodq1E3_aK3rhUrE,7612
 napari_tmidas/_tests/test_label_inspection.py,sha256=oUW4aJoM3ePEckZmPZNEwfDfob8brUsPGbfrHRnSL8c,2891
 napari_tmidas/_tests/test_processing_basic.py,sha256=Ua_7VSQ--D_cIT6ptupRsW6rN37BTyipT5mp4GX3BYI,19652
 napari_tmidas/_tests/test_processing_worker.py,sha256=X6F3Z2LH-7jd442wj1eerL8U1NS-BORV6SHTib7NsD4,4534
 napari_tmidas/_tests/test_reader.py,sha256=gN_2StATLZYUL56X27ImJTVru_qSoFiY4vtgajcx3H0,975
 napari_tmidas/_tests/test_regionprops_analysis.py,sha256=IGAEtdg83R9aH8wsINR8VCvNBgpYk6g3lH0S1IyBMLk,17030
-napari_tmidas/_tests/test_registry.py,sha256=Kf2G-8Y0mMRECDR-V_qpj-OMgQReBkFWyTHkGx6CRGQ,4504
+napari_tmidas/_tests/test_registry.py,sha256=0dVpeGE273YDPDy6KMInfkz2JAaJ_SUKFOySKn160_c,4795
 napari_tmidas/_tests/test_sample_data.py,sha256=D1HU_C3hWpO3mlSW_7Z94xaYHDtxz0XUrMjQoYop9Ag,104
 napari_tmidas/_tests/test_scipy_filters.py,sha256=SUcgyFh2IY4YVJvVO6_J1JdgkCsYdW36RgpHLkkp2vg,6268
 napari_tmidas/_tests/test_skimage_filters.py,sha256=TgvwcE_1kpdRzg5Hex9z9IoJc5Mt7IJjbpsdmZFiOGc,9869
@@ -33,10 +33,11 @@ napari_tmidas/_tests/test_split_channels.py,sha256=aMvjppoHlPAuwWLGYa1UcfBM_fvu0
 napari_tmidas/_tests/test_spotiflow.py,sha256=BLSaD8z8r2zbkYEGmfQ3JkSgw5OkvEORnSzpbkIIz4Y,2578
 napari_tmidas/_tests/test_tyx_display_fix.py,sha256=rhKbmM1rkPAAUeV3x3VuJkzXwEoqgi3Gtrxi1PP4ijs,4804
 napari_tmidas/_tests/test_ui_utils.py,sha256=jRHma8i_kWkZD8uvu98Z8Fw5NorocRvA_gjap93nb48,2464
+napari_tmidas/_tests/test_viscy_virtual_staining.py,sha256=iy7YnM65lQhn01UqEMsF6Bx9HJjWDBUm8V9SyMJIeZk,4567
 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=osXY9jSgDsrwFaS6ShPHP0wGRxMuX1mHRN9EDa9l41g,1891
+napari_tmidas/processing_functions/__init__.py,sha256=1yG17a_ddZXXc12uwB-PkwsBeQD7YvpyKHqc8sZAfgc,2325
 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
@@ -45,19 +46,21 @@ napari_tmidas/processing_functions/cellpose_segmentation.py,sha256=qChVwyvGL5nqX
 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=BymvHtFmiqh_eSuix6RtsfjJV7s0fD54OJuIt82sf8Q,13722
+napari_tmidas/processing_functions/intensity_label_filter.py,sha256=cTVCyEPWsPFyz0xdzDj2RwrQaXOzi_kCXUdo2WtwzeY,13887
 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
 napari_tmidas/processing_functions/scipy_filters.py,sha256=1Y69F5Pe-MEJPwQEs_6Ci3ncFuTKiRAuKRvDxmOQUPw,17871
-napari_tmidas/processing_functions/skimage_filters.py,sha256=Nhv6E8_YcRZ2s1FMkzDJNHr64fpMbUSHpUIY7nuvMHs,25192
+napari_tmidas/processing_functions/skimage_filters.py,sha256=og2mrEHNLBGQA6j07DHX94rhXJs4fRt5nzjpLyUmbeM,28154
 napari_tmidas/processing_functions/spotiflow_detection.py,sha256=2FLnDNXLc0eNj8vhp_XBv_bukX5pJOEhuiyXbUzzcyU,32811
 napari_tmidas/processing_functions/spotiflow_env_manager.py,sha256=07J_tYADMvIVIr_afniSNt8uEduecqpNblSWEj9aH7Q,20323
 napari_tmidas/processing_functions/timepoint_merger.py,sha256=7pXyfcI2rXZz6_TP3v_WejmMFivNVyUzkzBmifMiFKA,27424
 napari_tmidas/processing_functions/trackastra_tracking.py,sha256=IkFk5HoEZmKdcu5jXri4WMhHN1KTADDMxSpeYfPgSbo,9976
-napari_tmidas-0.2.5.dist-info/licenses/LICENSE,sha256=tSjiOqj57exmEIfP2YVPCEeQf0cH49S6HheQR8IiY3g,1485
-napari_tmidas-0.2.5.dist-info/METADATA,sha256=RR2asRsCVPnqhGfgiGer6_OPcL4T2fKdrpWOtEtJKG0,14951
-napari_tmidas-0.2.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napari_tmidas-0.2.5.dist-info/entry_points.txt,sha256=fbVjzbJTm4aDMIBtel1Lyqvq-CwXY7wmCOo_zJ-jtRY,60
-napari_tmidas-0.2.5.dist-info/top_level.txt,sha256=63ybdxCZ4SeT13f_Ou4TsivGV_2Gtm_pJOXToAt30_E,14
-napari_tmidas-0.2.5.dist-info/RECORD,,
+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-0.2.5.dist-info → napari_tmidas-0.3.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

napari_tmidas-0.2.5.dist-info/METADATA

@@ -1,282 +0,0 @@
-Metadata-Version: 2.4
-Name: napari-tmidas
-Version: 0.2.5
-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
-License: 
-        Copyright (c) 2025, Marco Meer
-        All rights reserved.
-        
-        Redistribution and use in source and binary forms, with or without
-        modification, are permitted provided that the following conditions are met:
-        
-        * Redistributions of source code must retain the above copyright notice, this
-          list of conditions and the following disclaimer.
-        
-        * Redistributions in binary form must reproduce the above copyright notice,
-          this list of conditions and the following disclaimer in the documentation
-          and/or other materials provided with the distribution.
-        
-        * Neither the name of copyright holder nor the names of its
-          contributors may be used to endorse or promote products derived from
-          this software without specific prior written permission.
-        
-        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-        
-Project-URL: Bug Tracker, https://github.com/macromeer/napari-tmidas/issues
-Project-URL: Documentation, https://github.com/macromeer/napari-tmidas#README.md
-Project-URL: Source Code, https://github.com/macromeer/napari-tmidas
-Project-URL: User Support, https://github.com/macromeer/napari-tmidas/issues
-Classifier: Development Status :: 2 - Pre-Alpha
-Classifier: Framework :: napari
-Classifier: Intended Audience :: Developers
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Operating System :: MacOS
-Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Topic :: Scientific/Engineering :: Image Processing
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy<2.0,>=1.23.0
-Requires-Dist: magicgui
-Requires-Dist: tqdm
-Requires-Dist: qtpy
-Requires-Dist: scikit-image>=0.19.0
-Requires-Dist: scikit-learn-extra>=0.3.0
-Requires-Dist: pyqt5
-Requires-Dist: zarr
-Requires-Dist: ome-zarr
-Requires-Dist: napari-ome-zarr
-Requires-Dist: nd2
-Requires-Dist: pylibCZIrw
-Requires-Dist: readlif
-Requires-Dist: tiffslide
-Requires-Dist: acquifer-napari
-Provides-Extra: testing
-Requires-Dist: tox; extra == "testing"
-Requires-Dist: pytest>=7.0.0; extra == "testing"
-Requires-Dist: pytest-cov; extra == "testing"
-Requires-Dist: pytest-qt; extra == "testing"
-Requires-Dist: pytest-timeout; extra == "testing"
-Requires-Dist: napari; extra == "testing"
-Requires-Dist: pyqt5; extra == "testing"
-Requires-Dist: psygnal>=0.8.0; extra == "testing"
-Provides-Extra: clustering
-Requires-Dist: scikit-learn-extra>=0.3.0; extra == "clustering"
-Provides-Extra: deep-learning
-Requires-Dist: torch>=1.12.0; extra == "deep-learning"
-Requires-Dist: torchvision>=0.13.0; extra == "deep-learning"
-Requires-Dist: timm; extra == "deep-learning"
-Requires-Dist: opencv-python; extra == "deep-learning"
-Requires-Dist: cmake; extra == "deep-learning"
-Requires-Dist: hydra-core; extra == "deep-learning"
-Requires-Dist: eva-decord; extra == "deep-learning"
-Provides-Extra: all
-Requires-Dist: napari-tmidas[clustering,deep-learning,testing]; extra == "all"
-Dynamic: license-file
-
-# napari-tmidas
-
-[![License BSD-3](https://img.shields.io/pypi/l/napari-tmidas.svg?color=green)](https://github.com/macromeer/napari-tmidas/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/napari-tmidas.svg?color=green)](https://pypi.org/project/napari-tmidas)
-[![Python Version](https://img.shields.io/pypi/pyversions/napari-tmidas.svg?color=green)](https://python.org)
-[![Downloads](https://static.pepy.tech/badge/napari-tmidas)](https://pepy.tech/project/napari-tmidas)
-[![DOI](https://zenodo.org/badge/698257324.svg)](https://zenodo.org/badge/latestdoi/698257324)
-[![tests](https://github.com/macromeer/napari-tmidas/workflows/tests/badge.svg)](https://github.com/macromeer/napari-tmidas/actions)
-
-This napari plugin consists of a growing collection of pipelines for fast batch processing of confocal and whole slide microscopy images of biological tissues. This is a WIP and based on the [T-MIDAS terminal](https://github.com/MercaderLabAnatomy/T-MIDAS).
-
-## Features
-Currently, **napari-tmidas** provides pipelines as widgets for batch image conversion and processing, object cropping, label image inspection and ROI colocalization (cf. [usage](#usage) below). You can request new batch image processing features in [issues](https://github.com/MercaderLabAnatomy/napari-tmidas/issues).
-
-## Installation
-
-(Video installation guides: https://www.youtube.com/@macromeer/videos)
-
-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]"
-
-Now you can install `napari-tmidas` via [pip]:
-
-    pip install napari-tmidas
-
-**For deep learning features** (Batch Crop Anything with SAM2, Spotiflow, Careamics, Trackastra), also install:
-
-    pip install 'napari-tmidas[deep-learning]'
-
-Or install everything at once:
-
-    pip install 'napari-tmidas[all]'
-
-It is recommended though to install the **latest development version**. Please also execute this command from time to time in the activated environment to benefit from newly added features:
-
-    pip install git+https://github.com/MercaderLabAnatomy/napari-tmidas.git
-
-### Additional Setup for Batch Crop Anything
-
-To use the Batch Crop Anything pipeline with SAM2, you need to install SAM2 separately:
-
-    cd /opt # if the folder does not exist: mkdir /opt && cd /opt
-    git clone https://github.com/facebookresearch/sam2.git && cd sam2
-    pip install -e .
-    curl -L https://dl.fbaipublicfiles.com/segment_anything_2/092824/sam2.1_hiera_large.pt -o checkpoints/sam2.1_hiera_large.pt
-    mamba install -c conda-forge ffmpeg # we also need ffmpeg
-
-If you want to batch compress image data using [Zstandard](https://github.com/facebook/zstd), use the package manager of your operating system to install it:
-
-   ~~sudo apt-get install zstd~~    # Pre-installed on Linux :man_shrugging:
-
-    brew install zstd            # for macOS (requires Homebrew)
-    pip install zstandard        # Windows with Python >= 3.7
-
-And you are done!
-
-## Usage
-
-To use the plugin, start napari in the activated virtual environment with this terminal command:
-
-    mamba run -n napari-tmidas napari
-
-You can then find the installed plugin in the Plugins tab.
-
-### Microscopy Image Conversion
-
-Converts `.lif, .nd2, .czi, .ndpi` and Acquifer data to TIF or OME-Zarr formats. Scan a folder, select files, and export with preserved spatial metadata.
-
-**Supported Formats:**
-- **TIF** - Standard format for compatibility
-- **OME-Zarr** - Recommended for large datasets, [spec v0.5](https://ngff.openmicroscopy.org/latest/) compliant with automatic physical metadata extraction (voxel sizes, spacing)
-
-<img src="https://github.com/user-attachments/assets/e377ca71-2f30-447d-825e-d2feebf7061b" alt="Microscopy Image Conversion Widget" style="width:75%; height:auto;">
-
-
-### Image Processing
-
-1. You start with entering the path to the folder containing the images to be processed (currently supports TIF, later also ZARR) and optionally a filter for filename suffix
-
-![image](https://github.com/user-attachments/assets/41ecb689-9abe-4371-83b5-9c5eb37069f9)
-
-2. After indexing the files, a table appears with the found images. You can click on them to inspect them in the viewer.
-
-![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.
-
-<img src="https://github.com/user-attachments/assets/cfe84828-c1cc-4196-9a53-5dfb82d5bfce" alt="Image Processing Widget" style="width:75%; height:auto;">
-
-
-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.
-
-
-#### Processing Function Credits
-
-The image processing capabilities are powered by several excellent open-source tools:
-- [Cellpose 4](https://github.com/MouseLand/cellpose): Advanced cell segmentation
-- [Trackastra](https://github.com/weigertlab/trackastra): Cell tracking and analysis
-- [VisCy](https://github.com/mehta-lab/VisCy): Virtual staining using deep learning
-- [CAREamics](https://github.com/CAREamics/careamics): Content-aware image restoration and enhancement
-- [Spotiflow](https://github.com/weigertlab/spotiflow): Accurate and efficient spot detection for fluorescence microscopy
-
-#### Processing Function Documentation
-
-Detailed documentation for specific processing functions:
-
-**Core Processing**
-- [Basic Processing Functions](docs/basic_processing.md) - Label and intensity operations, channel splitting/merging, time series
-- [Cellpose Segmentation](docs/cellpose_segmentation.md) - Deep learning cell/nucleus segmentation
-- [TrackAstra Tracking](docs/trackastra_tracking.md) - Cell tracking across time-lapse data
-- [VisCy Virtual Staining](docs/viscy_virtual_staining.md) - Virtual staining of phase/DIC images using deep learning
-
-**Analysis and Quality Control**
-- [Grid View: Intensity + Labels Overlay](docs/grid_view_overlay.md) - Visual QC for segmentation results
-- [Intensity-Based Label Filtering](docs/intensity_label_filter.md) - Filter labels by signal intensity
-- [Regionprops Analysis](docs/regionprops_analysis.md) - Extract quantitative properties from labels
-
-**Advanced Processing**
-- [Advanced Processing Functions](docs/advanced_processing.md) - Denoising (CAREamics), spot detection (Spotiflow), SciPy/scikit-image filters, compression, colocalization
-
-### Batch Label Inspection
-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 > Batch Label Inspection`, which automatically saves your changes to the existing label image once you click the `Save Changes and Continue` button (bottom right).
-
-<img src="https://github.com/user-attachments/assets/0bf8c6ae-4212-449d-8183-e91b23ba740e" alt="Batch Label Inspection Widget" style="width:75%; height:auto;">
-
-### Crop Anything
-
-This pipeline combines the Segment Anything Model (SAM2; supports YX, ZYX and TYX data) 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`. Cropping works like this: Enter 2D view and go to the first z slice where the object to be cropped is appearing. Activate/select the points layer and click on the object. Terminal shows progress. You can then proceed to select another object (always do this in 2D mode)
-
-<img src="https://github.com/user-attachments/assets/6d72c2a2-1064-4a27-b398-a9b86fcbc443" alt="Crop Anything Widget" style="width:75%; height:auto;">
-
-
-
-
-### 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.
-
-<img src="https://github.com/user-attachments/assets/2f9022a0-7b88-4588-a448-250f07a634d7" alt="ROI Colocalization Widget" style="width:75%; height:auto;">
-
-## Contributing
-
-Contributions are very welcome. Tests can be run with [tox], please ensure
-the coverage at least stays the same before you submit a pull request.
-
-## License
-
-Distributed under the terms of the [BSD-3] license,
-"napari-tmidas" is free and open source software
-
-## Issues
-
-If you encounter any problems, please [file an issue] along with a detailed description.
-
-[napari]: https://github.com/napari/napari
-[copier]: https://copier.readthedocs.io/en/stable/
-[@napari]: https://github.com/napari
-[MIT]: http://opensource.org/licenses/MIT
-[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
-[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
-[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
-[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
-[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
-[napari-plugin-template]: https://github.com/napari/napari-plugin-template
-
-[file an issue]: https://github.com/macromeer/napari-tmidas/issues
-
-----------------------------------
-
-This [napari] plugin was generated with [copier] using the [napari-plugin-template].
-
-<!--
-Don't miss the full getting started guide to set up your new package:
-https://github.com/napari/napari-plugin-template#getting-started
-
-and review the napari docs for plugin developers:
-https://napari.org/stable/plugins/index.html
--->
-
-[napari]: https://github.com/napari/napari
-[tox]: https://tox.readthedocs.io/en/latest/
-[pip]: https://pypi.org/project/pip/
-[PyPI]: https://pypi.org/