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# Surface Area 3D

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The Surface Area 3D plugin in Microscopy Image Browser (MIB) calculates planar surface areas of 3D objects in microscopy datasets, such as organelle contacts (e.g., mitochondria and ER). It detects objects using 26-point connectivity, computes surface areas from centerlines, and supports visualization and export to various formats.

## Overview

The plugin analyzes 3D objects by generating triangulated surfaces from cross-sectional centerlines.
Key features include:

- Detection of 3D objects with 26-edge connectivity.
- Calculation of surface areas per object.
- Export to MATLAB, Imaris, Amira, CSV, Excel, or MATLAB binary formats.
- Visualization of surfaces in MATLAB or MIB’s `Selection` layer.

## Parameters

Configure the analysis with these settings:

- Material with Surfaces select the model material to analyze. Objects are detected in 3D with 26-edge connectivity, and surfaces are generated per object.
- XY Smoothing smooth centerline points’ coordinates (XY plane) to refine profiles.
- XY Sampling increase triangle size by skipping points (e.g., 3 uses every third point for triangulation).
- Z Sampling similar to XY sampling, applied to Z-dimension.
- Show Points display detected points in the Selection layer. Clear afterward with `Shift`+`C` to avoid model conflicts.
- Export Results to MATLAB generate a structure in the main MATLAB workspace.

Configiration of the export structure

- `.pixSize`: dataset pixel size (`SurfaceArea(1).pixSize`).
- `.MaterialName`: analyzed material name (`SurfaceArea(1).MaterialName`).
- `.xySmoothValue`: XY smoothing factor.
- `.xySamplingStep`: XY sampling value.
- `.zSamplingStep`: Z sampling value.
- `.SumAreaTotal`: total area per surface (`SurfaceArea(N).SumAreaTotal`).
- `.PointsVector`: point indices per profile (`[x,y,z]`).
- `.PointCloud`: all points as `[index](x,y,z)`.
- `.Centroid`: object centroids.
- `.Area`: area between consecutive slices (cell array).

- Save Results save to MATLAB, Excel, or CSV.
- Add Material Name append material name to
  output filenames.
- Generate a Model for Each Contact save surfaces in AmiraMesh format to a folder.
- Export Contacts to Imaris export surfaces to Imaris (requires Imaris 8 and ImarisXT).

Warning

Clear the `Selection` layer after checking points (`Shift`+`C`) to prevent unintended changes to the model.

## Usage

Access the plugin via:
`Menu → Plugins → Organelle Analysis → Surface Area 3D`.

The following steps outline analysis, using an example of mitochondria-ER contacts:

Load Dataset and Model:

- Open a 3D dataset (e.g., Huh7.tif).
- Load a model with materials (e.g., Labels_Huh.model) via `Menu → File → Load model`.

Open from Menu

It is possible to load both the dataset and the model using
`Menu->File->Example datasets->SBEM->Huh7 and model (29 Mb)` (see more)

Help Resources

- Tutorial Video: Surface Area 3D Demo (Note: Video refers to plugin as ContactArea3D).
- External Tutorial: Plasmodesmata Analysis.

## Credits and Acknowledgements

Author: Ilya Belevich, University of Helsinki
- Version: 1.00, 13.02.2020
- Email: ilya.belevich@helsinki.fi

Big thanks to David Legland (Institut National de la Recherche Agronomique, France) for discussion about triangulation of points: function `mibTriangulateCurvePair.m` is based on `triangulateCurvePair.m` from MatGeom tools by David Legland

## How to Cite

If you use this plugin, please check for citation:
Data analysis pipeline in Paterlini, Belevich et al., 2020

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