Skip to content

Granularity

Back to MIB | User Interface | Plugins | Organelle Analysis

Overview

Granularity plugin

The Granularity plugin in Microscopy Image Browser (MIB) performs analysis of endoplasmic reticulum (ER) models to quantify the granularity of structures, i.e. ratio between sheets and tubules.
It supports customizable subarea selection, structuring element configuration, and export of results for further analysis.

Usage

Access the plugin via:
Menu → Plugins → Organelle Analysis → Granularity.

Follow these steps to analyze granularity:

Load Images and models of ER Dataset and model of ER

Start the plugin:
Menu → Plugins → Organelle Analysis → Granularity.

Select Analysis Mode: Mode

  • 2D, current slice only - use to preview 2D mode on the current slice
  • 2D, time-lapse - apply 2D analysis for the whole dataset
  • 3D, volume - apply 3D strel elements to do calculations in 3D space

Define Subarea: Subarea settings

  • Use Current View to update the X and Y fields using the currently shown area.
  • Click Subarea from Selection to restrict analysis to a selected area (drawn via MIB’s Selection tools).
  • Adjust coordinates manually in the subarea edit boxes or click Reset Dimensions to revert to the full image.

Select Materials: Select material

  • Click Update Materials to get the list of materials from the current model and update the Select material dropdown.
  • Use Select material to select material

Configure Structuring Element (Strel) Configure Structuring Element

  • Use Strel Type to select type of the structural element to use
  • Set Size XY (XY plane) and Z (for 3D) to define the shape of the structural element.
  • Specify Strel Rotations for number of strel rotations to use.

Info

Higher values ensure better results, but with increase of computation time.

  • Click Preview Strel to visualize the structuring element before analysis.

Export Results: Configure Structuring Element

  • Check MATLAB to export results to the main MATLAB workspace as a structure.
  • Check Save to a file to save results in MATLAB of EXCEL formats
  • Click ... to choose an output file (.xlsx for Excel or .mat for MATLAB).

Run Analysis:

Dataset and model of ER

  • Click Calculate to compute granularity metrics.
  • Results are displayed in the Image View panel.

Visualization of sheets (red) and tubules (yellow) compartments of ER

Credits

Back to MIB | User Interface | Plugins | Organelle Analysis