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# Measure Tool

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## Overview

Based on the Image Measurement Utility by Jan Neggers, Eindhoven University of Technology. This tool enables various length measurements and generates corresponding intensity profiles.

Note

Visualization of measurements can be switched on/off using the Ann/Measure checkbox in the View Settings panel.

## Measure panel

Defines the measurement type, started with the Add button.
Select the color channel for intensity profiles via the Color channel combo box.

### Examples of tools for manual measurement

- Angle: measures the angle between two lines.
  a) place the intersection point;
  b) place the second point to form the first line with the intersection;
  c) place the third point to form the second line with the intersection;
  d) adjust if needed; double-click above the line to accept.

- Caliper: measures the perpendicular distance from a line to a point.
  a) place two points to define the line;
  b) adjust if needed; double-click above the line to accept;
  c) place the point;
  d) adjust if needed; double-click above the point to accept.

- Circle: measures the radius of a circle.
  a) place a point at the circle’s center;
  b) place a point at the edge;
  c) adjust if needed; double-click above the circle to accept.

- Distance (freehand): measures the length of a path.
  a) select interpolation type with the Interpolation combo box;
  b) press Add;
  c) draw the path;
  d) convert to polyline, providing a factor to reduce vertices;
  e) adjust if needed; double-click above the path to accept.

- Distance (linear): measures the distance between two points.
  a) place the first point;
  b) place the second point;
  c) adjust if needed; double-click above the line to accept.

- Distance (polyline): measures a path with a set number of vertices.
  a) set vertex count with the Number of points edit box;
  b) select interpolation type with the Interpolation combo box;
  c) press Add;
  d) place the defined number of points;
  e) adjust if needed; press `A` and use the left mouse button to add a vertex, then double-click above the path to accept.

- Point: places a single point.
  a) place a point;
  b) adjust if needed; double-click above the point to accept.

- Fine-tuning: allows position adjustments during placement.
- Calculate intensities: generates an intensity profile for each measurement.
- Edit info: automatically show a dialog to provide additional information related to an added measurement
- Preview intensity (Distance, linear only): shows an intensity profile during placement.
- Integrate (Distance, linear only): integrates multiple points for intensity profiles, with point count set via the Width edit box.
- fixed number of points (freehand mode only): skips the vertex reduction dialog.
- Number of points (freehand and polyline modes): sets the number of points to place.

## Plot panel

Controls which measurement parts display in the Image View panel.
Customize line and marker appearance with the Options button.

## Voxel sizes panel

Shows voxel dimensions of the dataset. Update them with the Update button.

## Results panel

Displays measurement results.
Filter types with the Filter combo box.
Intensity profiles for selected measurements appear in a plot below the table.
With Jump on selection checked, the Image View panel centers on the selected measurement.

Right-click a selected item for a context menu:

- Jump to measurement: centers the selected measurement in the Image View panel.
- Modify measurement: enters edit mode to adjust shape and size.
- Recalculate selected measurements...: updates distances and intensity profiles if pixel size or color channels change.
- Duplicate measurement: duplicates the measurement.
- Generate kymograph: creates a depth projection image under the profile (linear, polyline, freehand only), previewable or savable in TIF, MATLAB, or CSV formats.
  Tutorial
- Plot intensity profile: plots intensity profile in a new figure.
- Delete measurement: removes the measurement from the list.

## Buttons at the bottom of the window

- Load: loads a measurement structure from a file or MATLAB workspace.
- Save: saves measurements and intensity profiles to a file (MATLAB or Excel) or MATLAB workspace.
- Refresh table: refreshes the measurement table.
- Delete all: removes all measurements.
- ?: opens this help page.
- Add: adds a new measurement of the type selected in the Measure panel.

Note

you can use `M` key shortcut to start selected measurement

- Close: closes the tool.

## Reference

- Image Measurement Utility by Jan Neggers

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