SLIM Plotter

Latest Version
2009 Apr 27

The SLIM Plotter is a tool for interactive visualization and inspection of combined spectral lifetime (SLIM) data, written by Curtis Rueden and Eric Kjellman. It uses the VisAD Java visualization toolkit to display data. It was originally developed for internal use within LOCI and the White and Keely labs, but has grown into an application that may be useful to others as well.

SLIM Plotter works with data in Becker & Hickl's SDT format (but could be adapted to work with data in other formats without too much extra effort). The main purpose of the program is to allow exploration of regions of data collected with a combined spectral lifetime detector.

The right-hand plot shows an intensity image for each channel (controlled with the slider directly beneath the image). The left-hand plot shows the lifetime histograms for each channel, rendered as a surface. Individual channels can be toggled using the checkbox next to the slider beneath the right-hand plot.

Optionally, SLIM Plotter can fit single-exponential curves to the lifetime data, to determine an approximation of the aggregate lifetime value per channel, using the Levenberg-Marquardt least squares curve fitting algorithm (LMA). To use this feature, the "Align peaks" option must be checked when the data is first read—so that SLIM Plotter can adjust for slight discrepancies in the system response time between channels. The log window on the bottom right shows the results of this alignment, as well as the exact parameter values of the curve fits.

SLIM Plotter functions similarly for single-channel lifetime data, but uses a 2D line plot for the lifetime histogram, rather than a surface in 3D.

The lifetime histograms displayed in the left-hand plot are a summation of the pixels selected in the right-hand intensity view. By default, all pixels are selected, but the user can draw a region of interest (ROI) using the mouse to focus on a particular area. Individual pixels can be selected with a mouse click. The text above the left-hand plot details the portion of pixels currently selected, as well as the minimum and maximum aggregate lifetime values across all channels (if known).

Lastly, the lifetime histograms currently being viewed can be exported to a simple text file for further processing in another program, such as a spreadsheet.

Instructions

SLIM Plotter requires the Java Runtime Environment and Java3D.

Windows

  1. Verify whether you have Javainstalled.
  2. Download and install Java3D.
  3. Unzip slim.zip into your "Program Files" folder. A subfolder called "SlimPlotter" will be created.
  4. Double-click on SlimPlotter.exe to launch the program.

Mac OS X

  1. SLIM Plotter requires Mac OS X 10.3 "Panther" or greater:
    • If you are running 10.4 "Tiger" or later, everything you need is already installed.
    • If you are running 10.3 "Panther," install the Java3D and JAI update from Apple.
  2. Expand slim.zip, if your browser did not do so already. Drag the resulting "SlimPlotter" folder to your Applications folder.
  3. Double-click on SlimPlotter to launch the program.

Linux

  1. Verify whether you have Javainstalled.
  2. Download and install Java3D.
  3. Unzip slim.zip wherever you like (your home directory works well). A subfolder called "SlimPlotter" will be created.
  4. You can launch SLIM Plotter from the command line with the included slim script.
Language
Java