Metadata-Version: 2.1
Name: PartSeg
Version: 0.12.2
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/roi_analysis.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-lastest-windows.zip) (build on Windows 10)
            -   [Linux](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-lastest-linux.zip) (build on Ubuntu 18.04)
            -   [MacOS](https://4dnucleome.cent.uw.edu.pl/PartSeg/Downloads/PartSeg-lastest-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
        
        ## napari plugin
        
        PartSeg provides napari plugins for io to allow read projects format in napari viewer.
        
        ## 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/roi_analysis.png)
        
        Main window of Segmentation Analysis with view on measurement result:
        
        ![interface](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/roi_analysis2.png)
        
        Window for creating set of measurements:
        
        ![statistics](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/measurement.png)
        
        Main window of Mask Segmentation:
        
        ![mask interface](https://raw.githubusercontent.com/4DNucleome/PartSeg/master/images/roi_mask.png)
        
        ## Laboratory
        
        Laboratory of functional and structural genomics
        [http://4dnucleome.cent.uw.edu.pl/](http://4dnucleome.cent.uw.edu.pl/)
        
        
        ## Changelog
        
        ### 0.12.2
        
        -   Fix windows bundle
        
        ### 0.12.1
        
        -   History of last opened files
        -   Add ROI annotation and ROI alternatives
        -   Minor bugfix
        
        ### 0.12.0
        
        -   Toggle multiple files widget in View menu
        -   Toggle Left panel in ROI Analysis in View Menu
        -   Rename Mask Segmentation to ROI Mask
        -   Add documentation for interface
        -   Add Batch processing tutorial
        -   Add information about errors to batch processing output file
        -   Load image from the batch prepare window
        -   Add search option in part of list and combo boxes
        -   Add drag and drop mechanism to load list of files to batch window.
        
        ### 0.11.5
        
        -   add side view to viewer
        -   fix horizontal view for Measurements result table
        
        ### 0.11.4
        
        -   bump to napari 0.3.8 in bundle
        -   fix bug with not presented segmentation loaded from project
        -   add frame (1 pix) to image cat from base one based on segmentation
        -   pin to Qt version to 5.14
        
        ### 0.11.3
        
        -   prepare for napari 0.3.7
        -   split napari io plugin on multiple part
        -   better reporting for numpy array via sentry
        -   fix setting color for mask marking
        
        ### 0.11.2
        
        -   Speedup image set in viewer using async calls
        -   Fix bug in long name of sheet with parameters
        
        ### 0.11.1
        
        -   Add screenshot option in View menu
        -   Add Voxels measurements
        
        ### 0.11.0
        
        -   Make sprawl algorithm name shorter
        -   Unify capitalisation of measurement names
        -   Add simple measurements to mask segmentation
        -   Use napari as viewer
        -   Add possibility to preview additional output of algorithms (In View menu)
        -   Update names of available Algorithm and Measurement to be more descriptive.
        
        ### 0.10.8
        
        -   fix synchronisation between viewers in Segmentation Analysis
        -   fix batch crash on error during batch run, add information about file on which calculation fails
        -   add changelog preview in Help > About
        
        ### 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: Development Status :: 3 - Alpha
Classifier: Framework :: napari
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: pyqt
Provides-Extra: pyqt5
Provides-Extra: pyside
Provides-Extra: pyside2
Provides-Extra: test
