Installation and Getting Started

Python Versions: Python 3

Platforms: Windows, OSX, and Linux

PyPI package name: flika

dependencies: numpy, scipy, qtpy, pandas, matplotlib, pyqtgraph, scikit-image, scikit-learn, ipykernel, qtconsole, pyopengl, nd2reader.


Install on Windows and Mac OSX

flika requires Python 3 to run. To install Python along with most of flika’s dependencies, download Anaconda for the latest Python 3 version. Once Python is installed open a terminal and run:

pip install flika

Install on Linux

Make sure that the ‘pip’ command is for Python 3. Then open a terminal and run:

pip install flika

Starting flika

If flika was installed using pip, start flika by opening a terminal and typing:


If you want to access the variables inside flika with the command line, type:

from flika import *

For more information on starting flika, go to Starting flika.

Our first test run

Let’s generate a random image and apply a gaussian blur. If you are only interested in flika’s gui features, go to Image->Stacks->Generate Random Image. Once the image is generated, apply a gaussian blur to the current window by going to Process->Filters-> Gaussian Blur.

If you want to do the same thing by code, either use the console you ran the start_flika() command in or open the Script Editor (Scripts->Script Editor) and type:


Where to go next

Here are a few suggestions where to go next: