Leading Edge Intensity  and Calculations 

JFilament
Speckle TrackerJ
Leading Edge Position and Velocity
Leading Edge Intensity
Correlation Analysis
Speckle Velocities

Total Intensity:

The plugin Intensity_Ribbon calculates the total intensity in a "ribbon" of user-defined
width along the arc length of the leading edge for a selected image stack. Like LE_Velocity it requires a snake file generated in JFilament to indicate the position of the cell's leading edge. Also, like LE_Velocity, it maps contours to polar coordinates. When  Intensity_Ribbon is run it will prompt the user to input necessary data:

parameters

The required parameters are:

The user is then prompted to choose a snake file.

Outputs:

Data file: The file contains a matrix of intensities of dimentions N x 360. The x-coordinate of this matrix indicates the frame number, while the y coordinate of this matrix indicates angle. The total intensity is measured in intensity units of original image. The plugin does not subtract background intensity.

Image stack: 
The generated stack of 'ribbons' of lamellipodia displays Intensity as a function of angle and distance from leading edge, for all time frames. Below, an example is shown where the outer and inner boundaries of the  measuring 'ribbon' of lamellipodium are drawn in red and green, respectively.
Intensity Ribbon Example


Intensity_Profile:

The Intensity_Profile plugin calculates the intensity as a function of distance from the leading edge
for a selected image stack. Like Intensity_Ribbon it requires a snake file generated in JFilament to indicate the position of the cell's leading edge, and maps contours to polar coordinates. When  Intensity_Profile is run it will prompt the user to input necessary data:


Intensity Profile Parameter Input
The required parameters are:
Once the user inputs these data, Intensity_Profile will prompt the user to choose a snake file.

Outputs:

Data file: The file containing intensity measurements as functions of time, angle, and distance from the leading edge. The data is formatted in columns that provide: time(s), angle (degrees), distance from the leading edge (
Ám), and intensity. The plugin does not subtract background intensity. 

Image Stack: The intensity of each pixel is the average intensity calculated over the provided range of angles. 
The y-position of each image in the stack indicates the distance from the leading edge, and each frame is a different time.

References:


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