PartSeg is python GUI for bio imaging analysis

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  • License: GNU General Public License v3 or later (GPLv3+)
  • Author: Grzegorz Bokota
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Project description

PartSeg

Build Status PyPI version Documentation Status Build Status DOI Total alerts Language grade: Python Codacy Badge Requirements Status

PartSeg is gui and library for segmentation algorithms.

This application is designed to help biologist with segmentation based on threshold and connected components

interface

Tutorials

  • Tutorial: Chromosome 1 (as gui) link
  • Data for chromosome 1 tutorial link
  • Tutorial: Different neuron types (as library) link

Installing

  • From binaries:

    • Windows (build on Windows 10)
    • Linux (build on Ubuntu 18.04)
    • MacOS (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

Main window of Segmentation Analysis:

interface

Main window of Segmentation Analysis with view on measurement result:

interface

Window for creating set of measurements:

statistics

Main window of Mask Segmentation:

mask interface

Laboratory

Laboratory of functional and structural genomics http://4dnucleome.cent.uw.edu.pl/

Project details

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  • License: GNU General Public License v3 or later (GPLv3+)
  • Author: Grzegorz Bokota
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Release history Release notifications | RSS feed

0.16.0a1 pre-release

0.15.4

0.15.4b7 pre-release

0.15.4b6 pre-release

0.15.4b5 pre-release

0.15.4b4 pre-release

0.15.4b3 pre-release

0.15.4b2 pre-release

0.15.4b1 pre-release

0.15.4b0 pre-release

0.15.3

0.15.3a5 pre-release

0.15.3a4 pre-release

0.15.3a3 pre-release

0.15.3a2 pre-release

0.15.2

0.15.1

0.15.0

0.14.6

0.14.5

0.14.4

0.14.3

0.14.2

0.14.1

0.14.0

0.13.15

0.13.14

0.13.13

0.13.12

0.13.11

0.13.10

0.13.9

0.13.8

0.13.7

0.13.6

0.13.5

0.13.4

0.13.3

0.13.2

0.13.1

0.13.0

0.12.7

0.12.6

0.12.5

0.12.4

0.12.3

0.12.2

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0.12.0

0.12.0a0 pre-release

0.11.5

0.11.3

0.11.2

0.11.1

0.11.0

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0.10.8

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0.10.6

0.10.5

0.10.4

0.10.3

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0.9.7

This version

0.9.6

0.9.5

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0.9.3.post4

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0.9.3.post2

0.9.3.post1

0.9.2.3

0.9.2.2

0.9.2.1

0.9.2

0.9.1

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0.9b2 pre-release

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0.8.6

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0.8

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