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README.md

THIS PROJECT IS NOW UNMAINTENED AND DEPRECATED

Objects detection and robust tracking for cell biology

scikit-tracker aims to be a robust Python library to work with cell biology microscopy images. OME XML and OME Tiff are supported to handle input/output to the lib. The two main goals of the library is to implement detection and tracking algorithms relevant to analyse biological microscopy dataset.

Several algorithms are featured and it is planned to add others:

scikit-tracker provides several intuitive graphical interfaces to semi-manually modify detected objects and trajectories (thanks to Qt4).

Documentation

Current stable version is v0.2.

Dependencies

  • Python >= 2.7 and >= 3.3
  • numpy >= 1.8
  • scipy >= 0.12
  • pandas >= 0.13
  • scikit-image >= 0.9
  • scikit-learn >= 0.13
  • matplotlib >= 1.3

Optional

  • PyQt4

For developers

  • nose >= 1.3
  • sphinx >= 1.2
  • coverage >= 3.7

Installation

You can install scikit-tracker using pip:

$ pip install scikit-tracker

Or by cloning this repo and using setup.py:

$ git clone git@github.com:bnoi/scikit-tracker.git
$ python setup.py install

Authors

Licence

See LICENSE.

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