Module to identify intranuclear proteins on basis of fluorescence images.
Project description
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.
Note
The current release is a very early alpha version. Please report report any detected bugs and/or improvement suggestions.
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
$ git clone https://github.com/SilMon/NucDetect.git
or pypi
python3 -m pip install NucDetect
Start
The program can be started by running the NucDetectAppQT.py:
cd %UserProfile%/AppData/local/Programs/Python/python37/Lib/site-packages/gui
python -m NucDetectAppQT
Supported Image Formats
Following image formats are supported by NucDetect:
- TIFF
- PNG
- JPG
- BMP
Author: Romano Weiss
Co-Author: Stefan Rödiger
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