Metadata-Version: 2.1
Name: PartSeg
Version: 0.10.7
Summary: PartSeg is python GUI for bio imaging analysis especially nucleus analysis,
Home-page: https://4dnucleome.cent.uw.edu.pl/PartSeg/
Author: Grzegorz Bokota
Author-email: g.bokota@cent.uw.edu.pl
License: BSD-3-Clause
Project-URL: Documentation, https://partseg.readthedocs.io/en/stable/
Project-URL: Source Code, https://github.com/4DNucleome/PartSeg
Description: # PartSeg
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        PartSeg is gui and library for segmentation algorithms.
        
        This application is designed to help biologist with segmentation 
        based on threshold and connected components 
        
        ![interface](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/analysis_gui.png)
        
        ## Tutorials
        -   Tutorial: **Chromosome 1 (as gui)** [link](https://4dnucleome.cent.uw.edu.pl/PartSeg/tutorials/tutorial_chromosome_1/)
        -   Data for chromosome 1 tutorial [link](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg_samples.zip)
        -   Tutorial: **Different neuron types (as library)** [link](https://4dnucleome.cent.uw.edu.pl/PartSeg/tutorials/tutorial_diferrent_neurons/)
        
        ## Installing
        -   From binaries:
            -   [Windows](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.10.7-windows.zip) (build on Windows 10)
            -   [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.10.7-linux.zip) (build on Ubuntu 18.04)
            -   [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.10.7-macos.zip) (build on MacOS Mojave)
        
        -   With pip (on linux you need to install `numpy` and `cython` earlier) 
            -   From pypi: `pip install PartSeg[pyqt]`
            -   From repository: `pip install git+https://github.com/4DNucleome/PartSeg.git`
          
        ## Running 
        If you download binaries look for `PartSeg_exec` file inside the `PartSeg` folder 
        
        If you install from repository or from pip you cat run it with `PartSeg` command or `python -m PartSeg`. 
        First option do not work on Windows. 
        
        PartSeg export few commandline options: 
        -   `--no_report` - disable reporting errors to authors
        -   `--no_dialog` - disable reporting errors to authors and showing error dialog. Use only when running from terminal.
        -   `segmentation_analysis` - skip launcher and start analysis gui
        -   `segmentation` - skip launcher and start segmentation gui 
        
        ## Additional remarks
        PartSeg use current `imagecodecs-lite` as backed for `tifffile`. You may install full version if `imagecodecs` manually.  
        
        ## Save Format
        Saved project are tar files compressed with gzip or bz2 
        
        Metadata are saved in data.json file (in json format)
        images/mask are saved as *.npy (numpy array format)
        
        ## Interface
        Launcher. Chose program that you will launch:    
         
        ![launcher](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/launcher.png)
          
        Main window of Segmentation Analysis:
          
        ![interface](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/analysis_gui.png)
          
        Main window of Segmentation Analysis with view on measurement result:
          
        ![interface](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/analysis_gui2.png)
          
        Window for creating set of measurements:
           
        ![statistics](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/statisitcs.png)
          
        Main window of Mask Segmentation:
          
        ![mask interface](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/mask_gui.png)  
        
        ## Laboratory
        Laboratory of functional and structural genomics
        [http://4dnucleome.cent.uw.edu.pl/](http://4dnucleome.cent.uw.edu.pl/)
        
        
        ## Changelog 
        
        ### 0.10.7
        -   in measurements, on empty list of components mean will return 0
        
        ### 0.10.6
        -   fix border rim preview
        -   fix problem with size of image preview
        -   zoom with scroll and moving if rectangle zoom is not marked 
        
        ### 0.10.5
        -   make PartSeg PEP517 compatible.
        -   fix multiple files widget on Windows (path normalisation)  
        
        ### 0.10.4
        -   fix slow zoom
        
        ### 0.10.3
        -   deterministic order of elements in batch processing.
        
        ### 0.10.2 
        -   bugfixes 
        
        ### 0.10.1 
        -   bugfixes
        
        ### 0.10.0 
        -   Add creating custom label coloring.
        -   Change execs interpreter to python 3.7.
        -   Add masking operation in Segmentation Mask.
        -   Change license to BSD.
        -   Allow select root type in batch processing.
        -   Add median filter in preview.
        
        ### 0.9.7
        -   fix bug in compare mask
        
        ### 0.9.6 
        -   fix bug in loading project with mask
        -   upgrade PyInstaller version (bug  GHSA-7fcj-pq9j-wh2r) 
        
        ### 0.9.5
        -   fix bug in loading project in "Segmentation analysis"
        
        ### 0.9.4
        -   read mask segmentation projects 
        -   choose source type in batch
        -   add initial support to OIF and CZI file format
        -   extract utils to PartSegCore module
        -   add automated tests of example notebook
        -   reversed mask
        -   load segmentation parameters in mask segmentation
        -   allow use sprawl in segmentation tool
        -   add radial split of mask for measurement
        -   add all measurement results in batch, per component sheet  
        
        ### 0.9.3
        -   start automated build documentation
        -   change color map backend and allow for user to create custom color map. 
        -   segmentation compare
        -   update test engines
        -   support of PySide2 
        
        ### 0.9.2.3
        -   refactor code to make easier create plugin for mask segmentation 
        -   create class base updater for update outdated algorithm description
        -   fix save functions
        -   fix different bugs 
        
        ### 0.9.2.2
        -   extract static data to separated package
        -   update marker of fix range and add mark of gauss in channel control 
          
        ### 0.9.2.1
        -   add VoteSmooth and add choosing of smooth algorithm
        
        ### 0.9.2
        -   add pypi base check for update 
        
        -   remove resetting image state when change state in same image
        
        -   in stack segmentation add options to picking components from segmentation's
        
        -   in mask segmentation add:
            -   preview of segmentation parameters per component, 
            -   save segmentation parameters in save file
            -   new implementation of batch mode. 
        
        ### 0.9.1
        -   Add multiple files widget
        
        -   Add Calculating distances between segmented object and mask
        
        -   Batch processing plan fixes: 
            -   Fix adding pipelines to plan
            -   Redesign mask widget
        
        -   modify measurement backend to allow calculate multi channel measurements. 
        
        ### 0.9
        Begin of changelog
        
Keywords: bioimaging,GUI
Platform: Linux
Platform: Windows
Platform: MacOs
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 3 - Alpha
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: test
Provides-Extra: pysid2
Provides-Extra: pyqt5
Provides-Extra: pyqt
Provides-Extra: pyside
