Metadata-Version: 2.1
Name: PartSeg
Version: 0.9.6
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 :: 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 :: 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 (>=1.16.0)
Requires-Dist: tifffile (>=2019.7.26)
Requires-Dist: czifile (>=2019.4.20)
Requires-Dist: oiffile (>=2019.1.1)
Requires-Dist: imagecodecs-lite (>=2019.4.20)
Requires-Dist: appdirs (>=1.4.3)
Requires-Dist: SimpleITK (>=1.1.0)
Requires-Dist: scipy (>=0.19.1)
Requires-Dist: QtPy (>=1.3.1)
Requires-Dist: sentry-sdk (==0.13.1)
Requires-Dist: PyQt5 (>=5.10.1)
Requires-Dist: six (>=1.11.0)
Requires-Dist: h5py (>=2.7.1)
Requires-Dist: packaging (>=17.1)
Requires-Dist: pandas (>=0.22.0)
Requires-Dist: sympy (>=1.1.1)
Requires-Dist: Cython (>=0.29.13)
Requires-Dist: openpyxl (>=2.4.9)
Requires-Dist: xlrd (>=1.1.0)
Requires-Dist: PartSegData (==0.9.4)
Requires-Dist: defusedxml (>=0.6.0)

# 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-0.9.6-windows.zip) (build on Windows 10)
    -   [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.9.6-linux.zip) (build on Ubuntu 18.04)
    -   [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-0.9.6-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: `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/)


