Scripts that complement built-in commands related to image analysis. Scripts that deal with timelapse images are grouped under Time Series.

Detects particles in a multichannel image using TrackMate's LoG/DoG (Laplacian/Difference of Gaussian) segmentation

Extends the built-in command Analyze> Plot Profile to multichannel (composite) images. Features a Live mode, guesses displayed lookup tables and ignores disabled channels, i.e., those deselected in the "Channels" widget (which can be called by pressing Z, the shortcut for Image> Color> Channels Tool.

Notes:

• Y-axis upper limit is set by the active channel. If a profile from a brighter channel appears truncated, turn on Live mode, and activate the brighter channel using the C slider of the image.
• By default, rectangular areas and lines wider than 1 pixel are plotted using column averages. To use row averages instead Alt. This works in Live mode and mimics the behavior of the built-in Analyze> Plot Profile command. To use column averages at all times, activate the Vertical Profile checkbox in Edit> Options> Profile Plot Options...
• Live mode will stop as soon as a valid ROI (straight line or rectangular selection) stops being present. It will resume when a new new one is reinstated.
• If one of the channels uses an unconventional LUT, the script will plot its profile using black. To change the color of the plotted curves, turn on Live mode, activate the image, and apply a new LUT using the drop-down menu of the "Channels" widget.
• By default, the X-axis will use spatially calibrated distances. To use pixel distances instead hold down the Alt key when running the plugin from the BAR> Analysis> menu.

Extends the built-in command Image> Stack> Plot Z-axis Profile to multichannel images, while providing extra functionality such as Z-averaging (for 3D time sequences), choice of statistic to be plotted and ability to trigger custom routines while in live mode.

Notes:

• Intensities (mean, min, max or standard deviation) are retrieved from active ROI or entire canvas if no ROI exists
• With timelapse hyperstacks, intensities can be averaged across Z-slices at each time point
• Limits of Y-axis are automatically set to include data from all visible channels
• Similarly to Multichannel Plot Profile, only visible channels (those active in the Image>Color>Channels Tool widget) are plotted

A BeanShell script that extends the built-in command Analyze>Plot Profile by plotting a simple moving average of profiled data. It inherits most features of Multichannel Plot Profile. In Live mode, and with profiled image as the frontmost window, press press Ctrl to readjust the number of data points to be used in the SMA calculation.

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