Python implementation of TypiC: Typical Image Selection
Project description
typic is a python implementation of the Typical Image Chooser as described in
Markey, M.K., Boland, M.V., and Murphy, R.F. (1999) Towards Objective Selection of Representative Microscope Images. Biophysical Journal 76:2230-2237.
TypIC is also available as a service in the Protein Subcellular Location Image Database (PSLID); though the latter version is not the one described in this repository.
Master branch status
Development branch status
Pre-Requisites
numpy
scipy
To install the prerequisites in Ubuntu 12.04
sudo apt-get install update sudo apt-get install python-numpy python-scipy
Installation
There are several ways to install typic. The most common way is to download the source code, unzip/untar the source code package and run the command
sudo python setup.py install
I have plans of submitting this package to the Python Package Index. If I do so, then should be able to install it by running the command
sudo pip install typic
COMMENT: halcon depends on numpy and scipy. Installing these packages in Windows and MacOSX is not a trivial task. For more information refer to the documentation.
If you wish to install typic in a virtual enviroment, then you can do
virtualenv typic cd typic source ./bin/activate pip install numpy pip install scipy mkdir src cd src git clone git@github.com:icaoberg/typic.git cd typic python setup.py install cd ../../ deactivate
COMMENT: The previous snippet assumes that you have virtualenv installed in your working system.
Documentation
Documentation was written using Sphinx. To generate documentation use the following commands.
To generate html
cd docs make html
To generate PDF document
cd docs make latexpdf
To generate epub document
cd docs make epub
Bugs and Questions
To submit bugs about the source code visit
https://github.com/icaoberg/typic
To submit bugs about the documentation visit
https://github.com/icaoberg/typic-docs
For any other inquiries visit those links as well.
