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nucdetect

Python interface to detect and quantify intranuclear proteins

https://github.com/silmon/nucdetect

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.0%) to scientific vocabulary

Keywords

bioinformatics detection digital-image-processing dna-damage image-processing immunofluorescence pypi pyqt5 python python3 quantification skimage sqlite3
Last synced: 6 months ago · JSON representation

Repository

Python interface to detect and quantify intranuclear proteins

Basic Info
  • Host: GitHub
  • Owner: SilMon
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 71.1 MB
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
bioinformatics detection digital-image-processing dna-damage image-processing immunofluorescence pypi pyqt5 python python3 quantification skimage sqlite3
Created over 7 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

PyPI version Downloads

NucDetect - A python package for Detection and Quantification of DNA Doublestrand Breaks

NucDetect is a Python package for the detection and quantification of γH2AX and 53BP1 foci inside nuclei. Its written in pure Python 3.7, obeys the PEP 8 style guidelines and includes PEP 484 type hints as well as Epytext docstrings.

Result

Requirements

NucDetect is compatible with Windows, Mac OS X and Linux operating systems. It requires the following packages:

  • tensorflow>=2.1.0
  • numpy>=1.18.1
  • scikit-image>=0.16.2
  • matplotlib>=3.1.3
  • pyqt5>=5.14.1
  • numba>=0.48.0
  • pillow>=7.0.0
  • qtawesome>=0.6.1
  • piexif>=1.1.3

Installation

Run the following commands to clone and install from GitHub

console $ git clone https://github.com/SilMon/NucDetect.git

or pypi console python3 -m pip install NucDetect

Start

The program can be started by running the NucDetectAppQT.py: console cd %UserProfile%/AppData/local/Programs/Python/python37/Lib/site-packages/gui python -m NucDetectAppQT First start: Switch to the created NucDetect Folder, which will be created in User directory. Then place images you want to analyse into the images folder and click the reload button. This will load all images and create a thumbnail for each (needed to decrease the memory footprint of QT). This can take several minutes, depending on the number of images and used hardware (e.g. around 5 min for 2200 images on a Ryzen 3700X processor). Progress will be displayed in the command prompt.

Supported Image Formats

Following image formats are supported by NucDetect: * TIFF * PNG * JPG * BMP

Not supported

  • Grayscale images
  • Binary images

Wiki

Detailed information about the program can be found on the wiki

Supplementary Data

https://github.com/SilMon/NucDetectAdditionalData

Author: Romano Weiss

Co-Author: Stefan Rödiger

Owner

  • Login: SilMon
  • Kind: user
  • Location: Germany

Studied biotechnologist and enthusiast of digital image processing, machine learning and bioinformatics

GitHub Events

Total
  • Push event: 1
Last Year
  • Push event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 261
  • Total Committers: 4
  • Avg Commits per committer: 65.25
  • Development Distribution Score (DDS): 0.287
Past Year
  • Commits: 13
  • Committers: 1
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
SilMon w****o@w****e 186
SilMon w****m@b****e 47
SilMon r****s@b****e 26
devSJR s****r@b****e 2
Committer Domains (Top 20 + Academic)
b-tu.de: 3

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 months
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • dependabot[bot] (1)
  • SilMon (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 174 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 23
  • Total maintainers: 1
pypi.org: nucdetect

Module to identify intranuclear proteins on basis of fluorescence images.

  • Versions: 23
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 174 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.6%
Average: 23.2%
Stargazers count: 25.1%
Downloads: 29.4%
Forks count: 29.8%
Maintainers (1)
SilverMonkey
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • imagecodecs *
  • matplotlib >3.1.3
  • numba >0.48.0
  • numpy >1.18.2
  • piexif >=1.1.3
  • pillow >7.0.0
  • pyqt5 >5.14.1
  • pyqtgraph >0.10.0
  • qtawesome >0.6.1
  • scikit-image >0.16.2
  • tensorflow >2.2.0
setup.py pypi
  • matplotlib >3.1.3
  • numba >0.48.0
  • numpy >1.18.1
  • piexif >=1.1.3
  • pillow >7.0.0
  • pyqt5 >5.14.1
  • pyqtgraph >=0.11.1
  • qtawesome >0.6.1
  • scikit-image >0.16.2
  • tensorflow >2.2.0