Metadata-Version: 2.1
Name: PartSeg
Version: 0.9.2.2
Summary: PartSeg is python GUI for bio imaging analysis
Home-page: https://4dnucleome.cent.uw.edu.pl/PartSeg/
Author: Grzegorz Bokota
Author-email: g.bokota@cent.uw.edu.pl
License: UNKNOWN
Description: # PartSeg
        [![Build Status](https://travis-ci.org/4DNucleome/PartSeg.svg?branch=master)](https://travis-ci.org/4DNucleome/PartSeg)  
        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-0.9.2.2-windows.zip) (build on Windows 10)
          * [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.9.2.2-linux.zip) (build on Ubuntu 18.04)
          * [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.9.2.2-macos.zip) (build on MacOS Mojave) 
        * With pip (on linux you need to install `numpy` and `cython` earlier) 
            * From pypi: `pip install PartSeg`
            * From repository: 
              * `git clone git@github.com:4DNucleome/PartSeg.git`
              * `cd PartSeg/` 
              * `pip install -e .` 
         
        
        ## 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:
        Current version of PartSeg use `tifffile` package to read `*.tiff` files. Because newer version is easy to install
        only on Windows. If you install it manually with imagecodecs it should work.    
        
        
        ## 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/
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 3 - Alpha
Description-Content-Type: text/markdown
