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PIEZO1-LocalizationTools

This repository contains a collection of Python scripts and FLIKA plugins for analyzing PIEZO1 protein dynamics in microscopy data, as described in Bertaccini et al. 2024. The tools enable tracking, visualization, and analysis of PIEZO1 protein movement a

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PIEZO1-HaloTag Analysis Pipeline

This repository contains a collection of Python scripts and FLIKA plugins for analyzing PIEZO1 protein dynamics in microscopy data, as described in Bertaccini et al. 2024. The tools enable tracking, visualization, and analysis of PIEZO1 protein movement and activity in various cell types. It was created to help the Pathak lab (https://www.pathaklab-uci.com/) analyse TIRF recordings of PIEZO1 using flika (https://flika-org.github.io/).

Overview

The codebase is organized into two main components:

  • flika_plugins/: Custom plugins for the FLIKA image processing platform, providing interactive visualization and analysis tools
  • flika_scripts/: Command-line Python scripts for batch processing and analysis of PIEZO1 data
  • minimal_model/: Test data with results file from running the analysis pipeline

Key Features

  • Super-resolution tracking of PIEZO1-HaloTag puncta
  • Analysis of protein diffusion and mobility patterns
  • Visualization of protein localization and trajectories
  • Statistical analysis of protein behavior

Requirements

  • Python 3.7+
  • FLIKA (https://github.com/flika-org/flika)
  • Dependencies:
  • numpy
  • pandas
  • scipy
  • scikit-image
  • trackpy
  • PyQt5

Installation

  1. Install FLIKA following the instructions at: https://github.com/flika-org/flika

  2. Clone this repository: 

    git clone https://github.com/gddickinson/pathak_lab.git

  3. Install required Python packages: 

    pip install -r requirements.txt

  4. Install the FLIKA plugins:

  5. Copy the contents of flika_plugins/ to your FLIKA plugins directory
  6. Restart FLIKA to load the new plugins

Usage

The analysis pipeline consists of several steps:

  1. Preprocessing (flika_scripts/piezo1_analysis/1_preprocessing/)
  2. Convert and prepare microscopy data

  3. Bin data by frame

  4. Analysis (flika_scripts/piezo1_analysis/2_analysis/)

  5. Detect and track PI

[View full README on GitHub]