gddickinson / flika_plugins

flika plugin collection

flika_plugins

Python plugins written at UCI to expand to expand FLIKA (https://github.com/flika-org/flika)

Created for:

the Parker Lab (https://parkerlab.bio.uci.edu/)

the Pathak Lab (https://www.pathaklab-uci.com/)

HOW TO USE THE PLUGINS

Download the plugin folder, move it to the ~/.FLIKA/plugins directory and restart flika. http://flika-org.github.io/plugins.html

LIST of PLUGINS

• annotator Author: George Dickinson Function:

• centerSurroundROI Author: George Dickinson Function:

• detect_puffs Author: Kyle Ellefsen Function:

• dipoleAnalysis Author: George Dickinson Function:

• fft_Chunker Author: George Dickinson Function:

• fileLoader Author: George Dickinson Function:

• GlobalAnalysisPlugin Author: Function:

• lightSheet_tiffLoader Author: George Dickinson Function:

• light_sheet_analyzer Author: Kyle Ellefsen Function:

• linescan
  Author: George Dickinson Function:

• neuroLab_207 Author: George Dickinson Function:

• onTheFly_Reconstruction
  Author: George Dickinson Function:

• openCV Author: George Dickinson Function:

• overlay Author: George Dickinson Function:

• packageManager Author: George Dickinson Function:

• puffMapper Author: George Dickinson Function:

• pynsight Author: Kyle Ellefsen Function:

• quantimus Author: Kyle Ellefsen Function:

• rodentTracker Author: Kyle Ellefsen Function:

• roiExtras
  Author: George Dickinson Function:

• scaledAverageSubtract Author: George Dickinson Function:

• simulateMEPP Author: George Dickinson Function:

• simulatePuff Author: George Dickinson Function:

• synapse_plugin Author: George Dickinson (adapted from Brett Settle) Function:

• volumeSlider Author: George Dickinson (adapted from Kyle Ellefsen) Function:

• locsAndTracksPlotter Author: George Dickinson Function: Plots positions of tracked particles on tiff stack and provides analysis tools for localization data. Uses positions derived from pynsignt (Kyle Ellefsen), thunderStorm (https://zitmen.github.io/thunderstorm/) or trackpy (http://soft-matter.github.io/trackpy/v0.6.1/).

ABOUT

• Author: George Dickinson (Several of the plugins extended from original code by Kyle Ellefsen and Brett Settle)
• Date: August 23, 2020
• Lab: Ian Parker Lab, McGaugh Hall, UCI