Golgi Orientation

Overview

The Golgi Orientation plugin in Microscopy Image Browser (MIB) calculates the relative orientation of Golgi apparatus with respect to the nucleus surface or cell boundary in segmented 3-D microscopy models.

For each detected Golgi object the plugin computes a distance map from the reference structure (nucleus or cell boundary) and reports the standard deviation of the distance values sampled at all Golgi voxels. A low standard deviation indicates that the Golgi is concentrated at a uniform distance from the reference structure (well-oriented), while a high standard deviation indicates a more dispersed arrangement.

Results are saved as a MATLAB .mat file and, optionally, as a .csv or .xls spreadsheet.

A step-by-step video tutorial is available on YouTube : Golgi Orientation plugin tutorial

Two analysis modes are available:

Mode	Input	Best for
Complete model	A single 3-D dataset with separate model files for Golgi, nuclei, and cell outlines	Large volumes containing many cells
Cropped cells	One directory per cell, each containing one image and one multi-material model file	Per-cell crops prepared in advance

Launching the Plugin

Menu → Plugins → Organelle Analysis → Golgi Orientation

GUI Components

Mode and Information Panel

Mode selects the analysis mode:

Complete model — loads separate model files for the entire volume; switches to the Complete model files tab.
Cropped cells — processes a list of per-cell directories; switches to the Cropped cells dirs tab.

The information panel below the dropdown updates automatically to show step-by-step instructions for the selected mode.

Complete model files Tab

Visible when Mode is set to Complete model.

Image filename — full path to the image file. Click ... to browse.

Golgi model — path to the model file containing segmented Golgi objects. Each unique label index corresponds to one cell. Click ... to browse.

Nuclei model — path to the model file containing segmented nuclei (required for Relative to nucleus and Both methods). Click ... to browse.

Cell outlines model — path to the model file containing segmented cell boundaries (required for Relative to cell boundary and Both methods). Click ... to browse.

Model index convention

In Complete model mode the label index is used as a cell identifier: Golgi object 1005, nucleus 1005, and cell boundary 1005 all belong to the same cell. Make sure the three model files share the same labelling scheme.

Cropped cells dirs Tab

Visible when Mode is set to Cropped cells.

Input directories — list of directories to process. Each directory must contain exactly one image file and exactly one model file matching the selected filename extensions.

Add... — open a folder-picker dialog to add one or more directories to the list.

Remove selected — remove the currently highlighted directory from the list.

Remove all — clear the entire list.

Directory layout

Each directory should hold one cropped cell with a single-cell model containing the relevant materials at the indices specified in the Settings tab.

Settings Tab

Method

Method — orientation reference:

Relative to nucleus — distance map is computed from the nucleus surface.
Relative to cell boundary — distance map is computed from the outer cell boundary (inside-out, so voxels far from the boundary get large distances).
Both — compute both maps and report both standard-deviation columns.

Materials Panel (Cropped cells mode only)

Spinner indices that identify each structure inside a single-cell model file:

Golgi — material index of the Golgi (default: 3).

Nucleus — material index of the nucleus (default: 2).

Cell shape — material index of the cell outline (default: 1).

Size Threshold Panel (Complete model mode only)

Minimum object size filters applied before analysis to discard noise or artefacts:

Golgi — discard Golgi objects smaller than this value (in voxels, default: 0 = keep all).

Nucleus — discard nuclei smaller than this value (default: 0).

Cell shape — discard cell boundary objects smaller than this value (default: 0).

Distance from Nucleus Panel (Complete model mode only)

Distance from nucleus — crop margin added around each nucleus bounding box before computing the distance map, in voxels (default: 200). Increase this value if a warning appears that Golgi voxels lie outside the cropped region.

Filename Extensions and Output

Images — extension of image files to look up in each input directory when using Cropped cells mode (e.g. AM, TIF, H5).

Models — extension of model files (MODEL, TIF, TIFF).

Output filename — path and base name for the results file. Click ... to browse. The plugin always saves a .mat file; if the extension is .csv or .xls a spreadsheet is written as well.

Action Buttons

Calculate — run the analysis with the current settings.

Help — toggle the in-panel information text.

Close — close the plugin window and save the current settings to the MIB session so they are restored next time the plugin is launched.

Output Table

Complete model mode

Column	Description
Cell Id	Shared label index identifying the cell
Golgi stack Id	Index of the detected Golgi component (as originally found by `bwconncomp`)
Golgi index	Rank of this Golgi within the cell (1, 2, …)
Golgi volume, units	Golgi volume in physical units (width × height × depth voxel size)
Golgi volume, px	Golgi volume in voxels
Std relative to Nucleus	Std of distance-map values at Golgi voxels (nucleus reference)
Std relative to Cell boundary	Std of distance-map values at Golgi voxels (cell-boundary reference)
Nucleus volume, units	Nucleus volume in physical units
Nucleus volume, px	Nucleus volume in voxels
Cell volume, units	Cell volume in physical units
Cell volume, px	Cell volume in voxels

Cropped cells mode

Column	Description
Directory	Full path to the input directory
Directory short	Directory name only
Dataset name	Image filename
Model name	Model filename
Golgi stack Id	Index of the detected Golgi component
Volume, units	Golgi volume in physical units
Std relative to Nucleus	Std of nucleus-distance map values at Golgi voxels
Std relative to Cell boundary	Std of cell-boundary distance map values at Golgi voxels

Usage

Complete model mode

Segment Golgi, nuclei, and cell boundaries as separate model files in MIB. Use a consistent label index per cell across all three files (e.g. cell 1005 → Golgi label 1005, nucleus label 1005, cell outline label 1005).
Resample the dataset to isotropic voxels before computing 3-D distance maps.
Launch the plugin: Ribbon → Plugins → Organelle Analysis → Golgi Orientation.
Set Mode to Complete model.
Browse to the image and the three model files on the Complete model files tab.
Open the Settings tab and choose the Method. Adjust Distance from nucleus and size thresholds as needed.
Set the Output filename and the file extensions.
Click Calculate.

Tip

See below the download links for example datasets

Cropped cells mode

Segment each cell individually in MIB. In each cell's model file assign:
material index = Cell shape to the cell outline
material index = Nucleus to the nucleus
material index = Golgi to the Golgi
Save each cell as a separate directory with one image and one model file.
Resample to isotropic voxels.
Launch the plugin and set Mode to Cropped cells.
On the Cropped cells dirs tab click Add... and select all input directories.
On the Settings tab set the correct material indices and choose the Method.
Set Output filename and file extensions.
Click Calculate.

Example Datasets

Example datasets are available from Zenodo:

https://doi.org/10.5281/zenodo.21068508

The archive contains two test sets:

Cropped cells test set — three directories (BStem01, BStem02, BStem03), each with one image (AM format, 80 × 80 × 80 nm voxels) and one model file containing cell outline (material 1), nucleus (material 2), and Golgi (material 3).

Complete model test set — one directory with:

one image file (AM format, 80 × 80 × 80 nm voxels)
Labels_*_CellOutlines_as_objects.model — cell outlines, one label per cell
Labels_*_Golgi_as_objects.model — Golgi, matching labels
Labels_*_Nuclei_as_objects.model — nuclei, matching labels

Running the cropped-cells example

A step-by-step video tutorial is available on YouTube

Launch the plugin and set Mode to Cropped cells.
Click Add... and select the three BStem0* directories.
On the Settings tab keep the default material indices (Cell shape = 1, Nucleus = 2, Golgi = 3) and set Method to Both.
Set Output filename to a .xls or .csv path.
Click Calculate.

Running the complete-model example

A step-by-step video tutorial is available on YouTube

Set Mode to Complete model.
Browse to the image and the three model files.
On the Settings tab set Method to Both.
Click Calculate.

Citation

If you use this plugin in your research, please cite

Golgi organization regulates stem cell function in the small intestine

Ilya Belevich, Lucas Porcile, Agustin Sola-Carvajal, David Grommisch, Karl Annusvar, Paul Heinz, Srustidhar Das, Anna T. Webb, Simon Andersson, Nalle Pentinmikko, Eduardo J. Villablanca, James R. Goldenring, Maria Kasper, Eija Jokitalo, Robert J. Coffey, Pekka Katajisto, Sandra Scharaw

Nature Communications, 2026, accepted

Credits

Author: Ilya Belevich, University of Helsinki (ilya.belevich@helsinki.fi)
Part of: Microscopy Image Browser (https://mib.helsinki.fi)

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