Readme.md

PartSeg

PartSeg is gui and library for segmentation algorithms.

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

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[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

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:

Main window of Segmentation Analysis:

Main window of Segmentation Analysis with view on measurement result:

Window for creating set of measurements:

Main window of Mask Segmentation:

Laboratory

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