flika 0.2.1

An interactive image processing program for biologists written in Python.

## Flika ##

Flika is an interactive image processing program for biologists written in Python. ### Website ### [flika-org.github.io](http://flika-org.github.io/)

### Documentation ### [flika-org.github.io/documentation.html](http://flika-org.github.io/documentation.html)


### Installation Instructions ###

#### Windows #### If you aren’t comfortable manually installing Python packages, we have written a script that automates the following steps. You can find it at [https://github.com/flika-org/flika_windows_installer](https://github.com/flika-org/flika_windows_installer).

1. Install Python

   Flika requires Python 3 to run. To install Python, go [here](https://www.python.org/downloads/windows/) and download the latest Windows x86-64 MSI installer. Once the file is downloaded, double click the icon and follow the on-screen instructions.

2. Install Flika dependencies

   • numpy MKL

   • scipy

   • PyQt4

   • qtpy

   • pyqtgraph

   • scikit-image

   • xmltodict

   • ipython

   • zmq

   • ipykernel

   • qtconsole

   • pyopengl

   • nd2reader

   • openpyxl

   • matplotlib

   • tifffile

   There are many ways you can install these dependencies, but the following is the way we prefer. Once you have installed Python, make a folder on your Desktop called binary_dependencies. Go to [Christoph Gohlke’s website](http://www.lfd.uci.edu/~gohlke/pythonlibs/) and download the first three dependencies (numpy, scipy, and PyQt4) into the binary_dependencies folder. Make sure the computer architecture and python version match yours. For instance, I have Python 3.5 running on a 64 bit computer, so I downloaded numpy-1.12.0+mkl-cp35-cp35m-win_amd64.whl, scipy-0.19.0rc1-cp35-cp35m-win_amd64.whl, and PyQt4-4.11.4-cp35-cp35m-win_amd64.whl into the binary_dependencies folder. Once these three files are downloaded, open a command prompt (Start->cmd.exe), navigate to the binary_dependencies folder (cd Desktopbinary_dependencies) and run the following commands (replacing the numpy, scipy, and PyQt4 file names with your own): ` python -m pip install --upgrade pip pip install "numpy-1.12.0+mkl-cp35-cp35m-win_amd64.whl" pip install scipy-0.19.0rc1-cp35-cp35m-win_amd64.whl pip install PyQt4-4.11.4-cp35-cp35m-win_amd64.whl pip install qtpy pyqtgraph scikit-image xmltodict ipython zmq ipykernel qtconsole pyopengl nd2reader tifffile openpyxl `

   Now that all of Flika’s dependencies are installed you can remove the binary_dependencies folder and install Flika.

3. Install Flika

   Download the [zipped folder](https://github.com/kyleellefsen/Flika/archive/master.zip) from Github and extract the folder to a location on your computer (preferably in `C:/Program Files/`). After the folder has been extracted, you can run Flika with the command `python flika.py`. We recommend using the free IDE PyCharm for scripting in Flika. To run Flika in the PyCharm IPython interpreter, run the following command ` import os, sys; flika_dir = my_flika_dir; sys.path.append(flika_dir); from flika import *; start_flika() ` replacing `my_flika_dir` with the location of the flika folder.

#### Ubuntu #### 1. Install Python

Flika requires Python 3 to run. Make sure this is the version of Python you are using.

2. Install Flika dependencies

   Open a terminal and run the following commands: ` sudo apt-get install python-pip python-numpy python-scipy build-essential cython python-matplotlib python-qt4-gl libgeos-c1v5 libgeos-dev sudo pip install scikit-image `

3. Install Flika

   Download the [zipped folder](https://github.com/kyleellefsen/Flika/archive/master.zip) from Github and extract the folder to a location on your computer. Navigate to the directory Flika was downloaded into. Run Flika with the command

   `python flika.py`

#### Mac OSX ####

1. Install Python and Flika Dependencies

   Flika requires Python 3 to run. To install Python along with most of Flika’s dependencies, download [Anaconda](https://www.continuum.io/downloads) by Continuum.

2. Install Flika

   Download the [zipped folder](https://github.com/kyleellefsen/Flika/archive/master.zip) from Github and extract the folder to a location on your computer. Open a terminal (Press command+space, type ‘Terminal’). Navigate to the directory Flika was downloaded into. Run Flika with the command

   `python flika.py`