PartSeg is python GUI for bio imaging analysis especially nucleus analysis,

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  • License: BSD License (BSD-3-Clause)
  • Author: Grzegorz Bokota
  • Tags bioimaging , GUI
  • Requires: Python >=3.6
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Project 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

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/

Changelog

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

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