adaptation of bnoi/scikit-tracker to track cells

• numpy >= 1.8
• scipy >= 0.12
• pandas >= 0.13
• scikit-image >= 0.9
• scikit-learn >= 0.13
• matplotlib >= 1.8
• sktracker >= 0.2-dev

• ipython >= 2.0
• pyqt4 >= 4.10

First, install the requirements (except sktracker) from pip or anaconda.

The simplest way is to use anaconda, Once you installed anaconda, create a python 3 environment:

$ conda create -n py33 python=3.3 anaconda

And activate it:

$ source activate py33

Your bash prompt should now start with (py33) You'll need to install pyqt4 (make sure you're still within the py33 virtuall environment)

$ conda install pyqt4

The version of IPython is too hold for the UI tools in the notebooks, so if you want those, install the latest ipython with pip:

$ pip install --upgrade ipython

Now create a src directory where you'll clone scikit-tracker and cell-tracker:

$ mkdir src
$ cd src
$ git clone https://bnoi/scikit-tracker.git
$ cd scikit-tracker
$ python setup.py install
$ cd ..
$ git clone https://bnoi/cell-tracker.git
$ cd cell-tracker
$ python setup.py install

If it complains about gcc, try installing build-essentials (if you're using a debian-like distro).

In the cell-tracker source folder, you'll find a notebooks folder.

Copy it all somewhere in your home folder, that's where you'll use the code.

Start an ipython notebook (still under the py33 virtual environment):

$ ipython notebook

Navigate to the notebooks folder you just copied, and start with the Segmentation and Tracking notebook.