Metadata-Version: 2.1
Name: PartSeg
Version: 0.9.2
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
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
Requires-Dist: numpy
Requires-Dist: tifffile (<1,>=0.15)
Requires-Dist: appdirs
Requires-Dist: SimpleITK
Requires-Dist: PyQt5
Requires-Dist: scipy
Requires-Dist: QtPy
Requires-Dist: sentry-sdk
Requires-Dist: deprecation
Requires-Dist: qtawesome
Requires-Dist: six
Requires-Dist: h5py
Requires-Dist: pandas
Requires-Dist: sympy
Requires-Dist: Cython
Requires-Dist: openpyxl
Requires-Dist: xlrd

# 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_alpha-windows.zip) (build on Windows 10)
  * [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg_alpha-linux.zip) (build on Ubuntu 18.04)
  * [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg_alpha-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/




