A collection of Python plugins developed at UCI to extend FLIKA, an interactive image processing program for biologists.
These plugins were developed for research at:
- Download the desired plugin folder
- Move it to your
~/.FLIKA/pluginsdirectory - Restart FLIKA
- The plugin will appear in FLIKA's plugins menu
For detailed plugin installation instructions, visit the FLIKA documentation.
- annotator - Add annotations to image stacks
- detect_puffs - Calcium puff detection and analysis
- dipoleAnalysis - Analysis tools for dipole images
- fft_Chunker - FFT analysis on time-series data
- openCV - OpenCV-based image processing tools
- overlay - Image overlay and comparison tools
- centerSurroundROI - Create linked center and surround ROIs
- roiExtras - Additional ROI analysis capabilities
- linescan - Line scan analysis tools
- fileLoader - Extended file format support including ND2
- lightSheet_tiffLoader - Specialized light sheet TIFF loading
- packageManager - Plugin and dependency management
- pynsight - Single molecule localization
- quantimus - Quantitative image analysis
- rodentTracker - Animal tracking and behavior analysis
- locsAndTracksPlotter - Particle tracking visualization and analysis
- Compatible with:
- pynsight
- thunderStorm
- trackpy
- Compatible with:
- light_sheet_analyzer - Light sheet microscopy analysis
- onTheFly_Reconstruction - Real-time image reconstruction
- simulateMEPP - Miniature end-plate potential simulation
- simulatePuff - Calcium puff simulation
- GlobalAnalysisPlugin - Global data analysis tools
- puffMapper - Spatial analysis of calcium puffs
- scaledAverageSubtract - Background subtraction tools
- synapse_plugin - Synaptic activity analysis
- volumeSlider - 3D volume visualization and analysis
- neuroLab_207 - Neuroscience lab-specific tools
Contributions are welcome! Please feel free to submit a Pull Request.
This project is licensed under the MIT License - see the LICENSE file for details.
- George Dickinson
- Kyle Ellefsen
- Brett Settle
Several plugins were adapted or extended from original code by Kyle Ellefsen and Brett Settle.
For issues specific to these plugins, please use the GitHub issues system. For general FLIKA support, visit the FLIKA documentation.
Updates and changes are tracked in individual plugin directories.
If you use these plugins in your research, please cite both FLIKA and the specific plugin used.
- George Dickinson
- Institution: University of California, Irvine
- Lab: Ian Parker Lab, McGaugh Hall
- Date: August 23, 2020
Note: Each plugin directory contains detailed documentation specific to that tool.