Microscopy Image Browser Measure Tool

Measure Tool of MIB is based on Image Measurement Utility written by Jan Neggers, Eindhoven University of Technology. Using this tool it is possible to perform number of different length measurements and generate intensity profiles that correspond to these measurements.

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Contents

Overview

Note: the measurements can be switched on and off using the Annotation checkbox in the View Settings panel.

Measure panel

Define type of the measurement to perform, each measurement is started using the Add button. The color channel for intensity profile calculation can be specified using the Color channel combo box.

1. Angle: the angle of the intersection of two lines
a) place the intersection point;
b) place the second point that together with the intersection point form the first line;
c) place the third point that together with the intersection point form the second line;
d) adjust if needed; and double click above the line to accept
2. Caliper: the perpendicular distance between a line and a point
a) place two points that define the line;
b) adjust if needed; and double click above the line to accept;
c) place the point;
d) adjust if needed; and double click above the point to accept;
3. Circle: the radius of the circle
a) place a point at the center of a circle;
b) place a point at the edge of the circle;
c) adjust if needed; and double click above the circle to accept;
4. Distance (freehand): the length of a path
a) define type of interpolation using the Interpolation combo box;
b) press the Add button;
c) draw a path that should be measured;
d) convert path to a polyline; provide a factor to reduce number of vertices;
e) adjust if needed; and double click above the path to accept;
5. Distance (linear): the between two points
a) place the first point;
b) place the second point;
c) adjust if needed; and double click above the line to accept;
5. Distance (polyline): the length of a path defined with predefined number of vertices
a) define number of vertices using the Number of points edit box;
b) define type of interpolation using the Interpolation combo box;
c) press the Add button;
d) place defined number of points;
e) adjust the path if needed; press the "a" key and use the left mouse button to add a vertice to the path. Finally double click above the path to accept;
6. Point (polyline): place a point
a) place a point;
b) adjust the point if needed; double click above the point to accept;

Plot panel

The Plot panel defines which parts of measurements should be displayed in the Image View panel. Using the Options button look of these lines and markers can be specified.

Volel sizes panel

The Voxel sizes panel shows dimensions of voxels of the opened dataset. The voxels can be adjusted by pressing the Update button.

Results panel

This panel displays results of measurements. It is possible to filter types of the displayed measurements using the Filter combo box. The intensity profiles for the selected measurements are shown in a plot under the table. When the Jump on selection checkbox is selected the view in the Image View panel is automatically shifted to put selected measurement into the center of the panel.

Right click above the selected item starts a context menu with following options:

Buttons at the bottom of the window

Reference

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