file

Load Speckles: Load previous saved speckle trakcs.

Save Speckles: Save the current speckle tracks.

Append Speckles: Add speckles from another speckle file to existing speckles.

New Speckles: Remove all speckles.

image

Open Image Opens a new image.

macros

Batch locate and Track: Starts the Batch Tracker. Parameters are entered and then the program will proceed to try and locate all of the speckles marks for the frames specified.It will only locate speckles in the Selected Region.

Start ImageJ: This will start ImageJ if it was not already started and it will show the current image as an image stack. This will let you use ImageJ built in functions to filter and adjust the contrast.

Find Discontinuous: Selects a speckle track that is discontinuous. Discontinuous speckles tracks are tracks that have missing frames. Eg a speckle track that starts on frame five and ends on frame ten, but doesn't have a mark on frame six, would be selected and the image would be changed to frame five.

Measure Speckle Tracks: This macro uses the selected model to measure features of the selected speckle track. Using this function causes a window with a table of values to open. The columns of the data table are ordered as follows, frame, x, y, probability, weight-0,... The weight values are model dependent, and will be updated as nescessary. Two models that work with this feature are the Gaussian Fit model and the Adjustment model.
Gaussian Fit weight-0 is standard deviation, weight-1 is the amplitude, weight-2 is the offset of the gaussian used to fit the equation. If weight-1 and weight-2 are both zero, then a standard deviation within the range of values set in the parameters could not be found.
The Adjustment model weight-0 returns the average intensity within the Inner Radius at each speckle mark in the selected track.

models

Adjust Parameters: This will open up a dialog with all of the available parameters which can be adjusted. The parameters are broken into "Global" parameters which concern the program in general and "Model" parameters which concern the currently selected model.

Models: This is a list of available models. The selected one will be used when the "Auto-track" button is pressed. Models can be changed by pressing the up or down arrow keys.

about

Version: Shows the current version and date last built.