FLIKA Plugins Collection

A collection of Python plugins developed at UCI to extend FLIKA, an interactive image processing program for biologists.

Overview

These plugins were developed for research at:

• Parker Lab
• Pathak Lab

Installation

1. Download the desired plugin folder
2. Move it to your ~/.FLIKA/plugins directory
3. Restart FLIKA
4. The plugin will appear in FLIKA's plugins menu

For detailed plugin installation instructions, visit the FLIKA documentation.

Plugins

Image Analysis

• annotator - Add annotations to image stacks
• detect_puffs - Calcium puff detection and analysis (top level as detect_puffs_GDedit; the original is in NOT_WORKING_WITH_PY311/ and OLD/)
• dipoleAnalysis - Analysis tools for dipole images (in NOT_WORKING_WITH_PY311/)
• fft_Chunker - FFT analysis on time-series data
• openCV - OpenCV-based image processing tools
• overlay - Image overlay and comparison tools

ROI Tools

• centerSurroundROI - Create linked center and surround ROIs
• roiExtras - Additional ROI analysis capabilities
• linescan - Line scan analysis tools

File Management & Loading

• fileLoader - Extended file format support including ND2 (in NOT_WORKING/)
• lightSheet_tiffLoader - Specialized light sheet TIFF loading
• packageManager - Plugin and dependency management (in EXPERIMENTAL/)

Specialized Analysis

• pynsight - Single molecule localization (top level as pynsight_GDedit; the original is in NOT_WORKING_WITH_PY311/ and OLD/)
• quantimus - Quantitative image analysis (in OLD/)
• rodentTracker - Animal tracking and behavior analysis (in OLD/)
• locsAndTracksPlotter - Particle tracking visualization and analysis
  • Compatible with:
    • pynsight
    • thunderStorm
    • trackpy

Light Sheet Tools

• light_sheet_analyzer - Light sheet microscopy analysis (top level as light_sheet_analyzer_GDedit)
• onTheFly_Reconstruction - Real-time image reconstruction (in NOT_WORKING/)

Simulation

• simulateMEPP - Miniature end-plate potential simulation (in OLD/ as mepp_simulator)
• simulatePuff - Calcium puff simulation

Data Analysis

• GlobalAnalysisPlugin - Global data analysis tools (in EXPERIMENTAL/)
• puffMapper - Spatial analysis of calcium puffs (in EXPERIMENTAL/)
• scaledAverageSubtract - Background subtraction tools
• synapse_plugin - Synaptic activity analysis (in NOT_WORKING/)
• volumeSlider - 3D volume visualization and analysis

Specialized Applications

• neuroLab_207 - Neuroscience lab-specific tools (in OLD/)

The list above is not complete: the web catalogue below lists all 64 plugin folders (those with an info.xml), including the newer ones (spt_batch_analysis, thunderstorm_flika, kymograph_analyzer, flash_remover, ...) and the EXPERIMENTAL/, NOT_WORKING/, NOT_WORKING_WITH_PY311/, OLD/ and backups/ folders.

Web catalogue and demos

A browsable catalogue of every plugin, read from the repository itself (info.xml, README, and each Python file parsed with ast), with interactive demos of four pure-numpy analyses ported to JavaScript and run in the browser:

• Spot detection and localization: the spt_batch_analysis/thunderstorm_python pipeline on single frames (B-spline wavelet filter, std(Wave.F1) threshold, 4/8-neighbourhood local maxima, integrated-Gaussian LSQ/WLSQ fits, Thompson uncertainty) on a real TIRF frame from test_data/real (compared with the ImageJ ThunderSTORM localizations committed beside it) and synthetic frames with ground truth.
• Track features and directional autocorrelation: FeatureCalculator, GeometricAnalyzer, DirectionAnalyzer and AutocorrelationAnalyzer from spt_batch_analysis on committed tracks, random walks, drawn or pasted tracks.
• FFT in chunks: fft_Chunker's fft_chunks and group averages on the plugin's own test signal or a pasted trace.
• Kymograph speed and events: kymograph_analyzer's gradient velocity and threshold / z-score events on a synthetic kymograph with a known speed (kymograph extraction from a movie is not ported).

Each port is checked in node against the plugin's own Python (tests/fixtures/demo_cases.json, written by scripts/make_demo_fixture.py); the localization port reproduces the Python fits to better than 1e-6. Not ported: U-Track linking, the SVM classifier, MLE and multi-emitter fitting, puff detection, light-sheet reshaping and the deep-learning plugins (they need FLIKA, Qt or large libraries).

Static site: https://gddickinson.github.io/flika_plugins/ (built by .github/workflows/pages.yml).

Run it locally:

pip install -r requirements-web.txt
python run_web.py             # http://127.0.0.1:8198
python -m pytest -q tests     # catalogue, demos, fixture, regression tests and the node tests of the JS ports

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Authors

Primary Contributors

• George Dickinson
• Kyle Ellefsen
• Brett Settle

Acknowledgments

Several plugins were adapted or extended from original code by Kyle Ellefsen and Brett Settle.

Support

For issues specific to these plugins, please use the GitHub issues system. For general FLIKA support, visit the FLIKA documentation.

Version History

Updates and changes are tracked in individual plugin directories.

Citing

If you use these plugins in your research, please cite both FLIKA and the specific plugin used.

Contact

• George Dickinson
• Institution: University of California, Irvine
• Lab: Ian Parker Lab, McGaugh Hall
• Date: August 23, 2020

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Note: Each plugin directory contains detailed documentation specific to that tool.