Skip to content
A library for quantifying microbial colony growth using time series imaging
Python Jupyter Notebook
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
test
.gitignore
LICENSE
README.md
__init__.py
drawROI.py
equalizer.py
extractROI.py
gridder.py
gridder2.py
imgz.py
invader.py
segmenter.py
segmenter2.py
showmask.py
spotstats.py
spotz-simplified-template.ipynb
spotz.py
spotzplot.py

README.md

spotz

A library for quantifying microbial colony growth using time series imaging

Requirements

  • Numpy/Scipy/Matplotlib-- the standard Python numerical analysis stack

  • scikit-image -- a Python library for image processing

  • peakutils -- a Python library for detecting peaks in 1D data.

  • Click - A Python library for building command-line interfaces

Usage

spotz --help will show you the available commands. Each sub-command has it's own help page as well, e.g. unscanny gridder --help will show you the help page for the gridder sub-command.

You can’t perform that action at this time.