NucDetect 0.11.14.dev1

Module to identify intranuclear proteins on basis of fluorescence images.

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:

• scipy>=0.19.0
• numpy>=1.13.3
• scikit-image>=0.15
• matplotlib >= 3.0.2
• PyQT5 >= 5.11.3
• Pillow
• qtawesome
• piexif
• tensorflow >= 2.0
• numba >= 0.45.1

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

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Author: Romano Weiss

Co-Author: Stefan Rödiger