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# Threshold Analysis for Objects

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## Overview

The Threshold Analysis for Objects plugin in Microscopy Image Browser (MIB) performs shape and intensity threshold-based analysis of objects in microscopy images, calculating metrics such as size, intensity, or shape.It supports triangulation of object centroids, visualization of results, and export to Excel or MATLAB formats, making it useful for quantitative studies of cellular structures.

## GUI Components

### Selection of materials and threshold settings

Object of interest use this dropdown to select material of the model for analysis.
Alternatively, it is possible to provide indices of materials using an editbox on the right-hand side of the dropdown.

Color channel to use specify index of the color channel to be used for intensity calculations and thresholding

Threshold policy specify method to threshold the objects:

- Absolute provide thresholding value in the Threshold value field. All values that are above this value will be assigned to the Mask layer after press of the Start
- Relative allows to choose between Otsu and Median automatic thresholding options. Values above detected threshold will be assigned to the Mask layer. Note! it is possible to modify the threshold value by offsetting it using the Offset value editbox on the right-hand side.

Erode+Dilate additionally applies erosion and dilation operation to minimize thresholding noise and keeping only large thresholded structures.

Application of Erode+Dilate

Object connectivity select connectivity of the object detection, when `4` objects that are touching each other in the diagonal orientation will be split, otherwise (when `8`) fused together.

### Additional options

Calculate min diameter use this option to measure average thickness of objects. When Highlight as Selection is checked, the point used to measure mean thickness for each object are shown as the Selection layer. Use `Shift`+`C` to clear it after evaluation.

Triangulate centroids for multiple objects calculate the triangulated mesh where each edge in this mesh contains distance to the closest other object. This can be useful for analysis of distances between the objects. Remove free boundary facets can be used to remove edges that are connecting objects at the edges of the image producing too large connecting lines.

Remove free boundary facets example

### Export results

Make Plot generate a plot with results. It is possible to specify Figure Id to show the plot in a specific MATLAB window and start Autoprint dialog for automatic printing of the figure.

Example of the figure with results

MATLAB Workspace export results to the main MATLAB workspace as `ThreshAnalysis` and `ThreshAnalysisGraph` structures.

Fields

`ThreshAnalysis` has following fields:

        colCh
        materialId
        materialNames
        absoluteThresholdValue
        relativeThresholdMethod
        thresholdOffsetValue
        thresholdPolicy
        ErodeDilate
        pixSize
        datasetName
        modelName
        triangulatePoints
        triangulateRemoveFreeBoundary
        objConnectivity
        objId
        sliceNo
        objMaterialName
        CentroidX
        CentroidY
        FirstAxisLength
        SecondAxisLength
        Eccentricity
        Median
        TotalArea
        SliceName
        ThresholdedArea
        objThresholdValues
        RatioOfAreas
        minDiameter
        minDiameterAverage

graph with properties: `ThreshAnalysisGraph` is a graph object with the fillowing fields:

        Edges: [39×1 table]
        Nodes: [18×2 table]

Excel save results in Microsoft Excel format `.xls`

MATLAB format save results in MATLAB format `.mat`

Triangulation save results of object triangulation in MATLAB format `.mat`, Amira, or as Excel sheet.

... specify output filename for results.

Regenerate Output Path use this button to regenerate output filename relative to the open dataset. It is useful when processing multiple datasets one after another.

### Start calculations

Press the Start button to perform calculations.

## Usage

Access the plugin via:
`Menu → Plugins → Organelle Analysis → Thres Analysis for Objects`.

Follow these steps to analyze objects:

Load Image:

Prepare Model

- Create or load a model with segmented objects via `Segmentation table -> Load`.
- Use MIB’s `Segmentation` tools (e.g., `Brush`, `Threshold`, `Segment-anything model`) to segment objects.

Segmentation model

Start the plugin:

- `Menu → Plugins → Organelle Analysis → Thres Analysis for Objects`.
- Define suitable settings and export parameters

Plugin settings

Run Analysis:

- Click Start to segment objects and compute metrics.
- Results appear in MIB’s Image View panel or exported files.

Review Results:

Snapshot with results

Snapshot with Excel output table

## Credits

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

Back to MIB | User Interface | Plugins | Organelle Analysis