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.
Note 1: the measurements can be switched on and off using the Annotation checkbox in the View Settings panel.
Note 2: sometimes the tool may crash, in this case the Selection layter may be turned off. It is possible to enable it via Menu->File->Preferences->Disable selection->no.
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;
The fine-tuning checkbox: when selected positions of the measurements can be adjusted during the placement.
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.
The Voxel sizes panel shows dimensions of voxels of the opened dataset. The voxels can be adjusted by pressing the Update button.
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:
- Jump to measurement, select to shift the shown image so that the selected measurement is centered in the Image View panel;
- Edit measurement, select to trigger the edit mode to modify the shape and size of the measurement;
- Duplicate measurement, select to duplicate the measurement;
- Plot intensity profile, select to plot profile of intensities in a new figure.
- Delete measurement, select to remove measurement from the list
- Load - press to load from a file or import from the main Matlab workspace a structure with measurements;
- Save - press to save to a file (Matlab or Excel format) or export to the main Matlab workspace results of the measurements. The saved results contain both the measurements and intensity profiles;
- Refresh table - press to refresh the table with measurements;
- Delete all - press to remove all measurements;
- ? - press to call this help page
- Add - press to add a new measurement of the selected in the Measure panel type;
- Close - close the tool