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VolumeSlider

VolumeSlider is a powerful plugin for Flika, a Python-based image processing suite designed for bioimaging applications. This plugin specializes in the visualization, manipulation, and analysis of multi-dimensional image data, particularly 3D volumes and time se

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Overview

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Documentation

VolumeSlider Plugin for Flika

Overview

VolumeSlider is a powerful plugin for Flika, a Python-based image processing suite designed for bioimaging applications. This plugin specializes in the visualization, manipulation, and analysis of multi-dimensional image data, particularly 3D volumes and time series data commonly generated in light sheet microscopy and other volumetric imaging techniques.

Features

  • Multi-dimensional Data Visualization: Easily navigate through 3D volumetric data and time series.
  • Orthogonal View Display: Simultaneously view XY, XZ, and YZ planes of your volumetric data.
  • Data Transformation: Apply shear transformations to correct for light sheet angular distortions.
  • Overlay Capabilities: Compare multiple datasets by overlaying them with adjustable opacity and blending modes.
  • ROI Analysis: Analyze regions of interest with line profile tools and cross-sectional views.
  • DF/F0 Calculation: Calculate and visualize ratio changes for time series data.
  • 3D Visualization: View your data in 3D using scatter plots, texture plots, and volume rendering.
  • Export Options: Export data to various formats including Numpy arrays and Imaris (.ims) files.
  • Batch Processing: Process multiple files with consistent parameters for high-throughput analysis.

Installation

Prerequisites

  • Flika (latest version)
  • Python 3.6+
  • Required packages: numpy, PyQt5/PySide2, pyqtgraph, matplotlib, scikit-image, h5py, OpenGL

Setup

  1. Clone this repository into your Flika plugins directory: 

    git clone https://github.com/your-username/flika-volumeSlider.git ~/.flika/plugins/volumeSlider

  2. Start Flika and the plugin should appear in the plugins menu.

Usage

Getting Started

  1. Launch the Plugin: From Flika's menu, select Plugins → VolumeSlider → VolumeSlider
  2. Load Data: Choose to work with the current active wi

[View full README on GitHub]