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Tutorial    Large Cubes  Thin Cubes  Other Documentation

Data Cube Tool

A data cube is stack of images (as NIH Image does) or an image of vectors (a spectral image- each pixel is a vector of data). 

This tool, the Array of Circles Tool and the Mosaic Tool are designed to work with spectral images.


Large Data Cubes

Lispix opens large data cubes, such as spectrum images as a file-based cube window to conserve computer memory.  When opening such a cube for the first time, Lispix needs to preprocess these cubes, which takes several minutes.  Opening the cubes thereafter is very fast - faster than opening small data cubes in the old way (as a memory based cube).  If the spectrum images are small enough, Lispix gives you the choice of whether to open as a file cube, or as a memory based cube.  I recommend using the file cube, except for doing PCA (Principal Component Analysis), which still requires a memory based cube, as of 8/09.

You may wish to preprocess large data cubes in "batch mode" using *Data Cube* / Open / Preprocess Large Data Cubes.

Thin Data Cubes

As of 11/4/2010, Lispix will read 1-Dimensional SER or TIA files.  These are data cubes which are only one pixel high, in other words they consist of only one scan line.


 Single Slice Slider

The single slice slider appears under a freshly opened data cube window.  Right-clicking on the slider makes some convenient functions available for extracting a slice as an individual image (for thresholding or colorizing, for example), for setting the slice position exactly by typing (handy for deep data cubes where the precision of the slider is insufficient), and for moving the slider from cube to spectrum plots and back (handy for visualizing images within specific peaks on the spectrum plot).

Single slice slider:    Right-click on slider: 

Other Documentation



  • The top buttons work on the front cube.


  • The movie and registration buttons work on the cube selected by the cube! button - name of cube appears to right of button.




Illustration of summed image from a region of the spectrum.