1. 3D Hyperspectral Cubes Visualization
Asadollah Khoddam Mohammadi
Samaneh Omranian
Ghazal Azarfar
Nick Walter
Carol Hirschmugl

2. Objectives
Fourier Transform Infrared Imaging in conjunction with signal correction techniques is a powerful tool in chemical Analysis of micron size biological samples.
Synchrotron Imaging of a Dielectric Bead demonstrate the importance of electromagnetic shape resonances, and scattering
Accurate feature extraction and data interpretation can be done after signal correction

3. Introduction IR-Micro-Spectroscopy
IR spectroscopy is a widely used and versatile method for analysis at the molecular scale. Single molecular species are identified, and their amount quantified, by specific vibrational spectra with several characteristic absorption bands in the mid-IR range.
HDF files
The results of IR-Micro-Spectroscopy are saved into a single HDF file that contains a structured data, including absorption value of any point of the specimen due to applying different wave lengths.
Matlab Program
Matlab program can be used for reading the HDF files, processing data and showing data in visual 3D format.
Accurate extraction of chemical and structural features.
Determine characteristic absorbance of molecular vibrations from spectra

4. APPROACH Matlab program reads the 4D data file of size 128X128X128X389
Based on the selected wave length, and using adjustable threshold, the program finds the edges of the 3D surface and plots it as a 3D object that can be rotated in different angles.
Any sagittal, coronal, or axial slices can be selected for viewing in more details.
Any single point or a region of interest (ROI) can be selected for plotting wave length absorption plot.
The raw data can be integrated in a range of wave lengths and corrected to the baseline.

5. conclusion
The program uses the power of Matlab program in numerical analysis and data visualization.
The results and graphs show that Matlab is a good choice for programming environment of this project.
The GUI part of Matlab program requires more programming efforts than numerical analysis part.
Because of large data file, reading some part of the data into memory takes more time than calculations.
In the future the performance of the program could be enhanced by using parallel processing toolbox and GPU programming

6. Main Matlab GUI, including 3D view with its controls, slice view, wave length absorption view, and controls for changing the parameters