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

These details have not been verified by PyPI

Project links

Project description

PartSeg

Tests

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[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:

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

0.11.5

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

Project details

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Project links

Release history Release notifications | RSS feed

0.16.0a1 pre-release

Oct 22, 2024

0.15.4

Oct 1, 2024

0.15.4b7 pre-release

Sep 27, 2024

0.15.4b6 pre-release

Sep 20, 2024

0.15.4b5 pre-release

Sep 19, 2024

0.15.4b4 pre-release

Aug 13, 2024

0.15.4b3 pre-release

Aug 9, 2024

0.15.4b2 pre-release

Aug 1, 2024

0.15.4b1 pre-release

Jul 23, 2024

0.15.4b0 pre-release

Jul 15, 2024

0.15.3

Jul 10, 2024

0.15.3a5 pre-release

Jul 7, 2024

0.15.3a4 pre-release

Jul 6, 2024

0.15.3a3 pre-release

Jul 5, 2024

0.15.3a2 pre-release

Jul 4, 2024

0.15.2

Aug 28, 2023

0.15.1

Aug 8, 2023

0.15.0

May 30, 2023

0.14.6

Nov 13, 2022

0.14.5

Nov 9, 2022

0.14.4

Oct 24, 2022

0.14.3

Aug 18, 2022

0.14.2

May 5, 2022

0.14.1

Apr 27, 2022

0.14.0

Apr 15, 2022

0.13.15

Jan 18, 2022

0.13.14

Dec 1, 2021

0.13.13

Nov 28, 2021

0.13.12

Oct 22, 2021

0.13.11

Oct 13, 2021

0.13.10

Sep 15, 2021

0.13.9

Aug 11, 2021

0.13.8

Aug 11, 2021

0.13.7

Aug 2, 2021

0.13.6

Jun 25, 2021

0.13.5

May 6, 2021

0.13.4

Apr 17, 2021

0.13.3

Apr 16, 2021

0.13.2

Apr 1, 2021

0.13.1

Mar 31, 2021

0.13.0

Mar 8, 2021

0.12.7

Mar 2, 2021

0.12.6

Jan 14, 2021

0.12.5

Dec 30, 2020

0.12.4

Dec 28, 2020

0.12.3

Dec 22, 2020

0.12.2

Dec 18, 2020

0.12.1

Dec 6, 2020

0.12.0

Oct 27, 2020

0.12.0a0 pre-release

Oct 7, 2020

This version

0.11.5

Sep 30, 2020

0.11.3

Aug 29, 2020

0.11.2

Aug 6, 2020

0.11.1

Jul 22, 2020

0.11.0

Jul 20, 2020

0.11.0b2 pre-release

Jun 19, 2020

0.10.8

Apr 22, 2020

0.10.7

Apr 1, 2020

0.10.6

Apr 1, 2020

0.10.5

Mar 27, 2020

0.10.4

Mar 21, 2020

0.10.3

Mar 13, 2020

0.10.2

Mar 6, 2020

0.10.1

Mar 5, 2020

0.10.0

Mar 4, 2020

0.9.7

Feb 13, 2020

0.9.6

Jan 19, 2020

0.9.5

Jan 10, 2020

0.9.4

Nov 8, 2019

0.9.3.post5

Sep 16, 2019

0.9.3.post4

Sep 5, 2019

0.9.3.post3

Aug 19, 2019

0.9.3.post2

Aug 12, 2019

0.9.3.post1

Aug 8, 2019

0.9.2.3

May 22, 2019

0.9.2.2

Apr 18, 2019

0.9.2.1

Apr 16, 2019

0.9.2

Apr 4, 2019

0.9.1

Mar 20, 2019

0.9

Mar 6, 2019

0.9b2 pre-release

Mar 5, 2019

0.9b1 pre-release

Feb 28, 2019

0.8.6

Feb 22, 2019

0.8.4

Feb 13, 2019

0.8.3

Feb 7, 2019

0.8.2

Jan 15, 2019

0.8

Jan 14, 2019

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