ConfocalMicroscopyDemonstration

Synopsis

This IAC special project contains a demo for the visulaization image data generated by the confocal microscope.

Description

In the confocal microscope all structures out of focus are supressed when image is generated. This is obtained by an arangement of diaphragms which act as a point source and as a point detector at optically conjugated points in the path of the light rays. Rays out-of-focus are suppressed by the detection pinhole.
The depth of the focal plane is determined by the wavelength of the light, by the numerical aperture of the objective used, and the diameter of the diaphragm. At a wider detection pinhole the confocal effect can be reduced. To obtain a full image, the image point is moved across the specimen by mirror scanners. The emitted/reflected light passing through the detector pinhole is transformed into electrical signals by a photomultiplier and displayed on a computer monitor.

The data format used for this demo is NetCDF (Network Common Data Form). NetCDF is an abstraction that supports a view of data as a collection of self-describing, network-transparent objects that can be accessed through a simple interface. Array values may be accessed directly, without knowing details of how the data is stored. Auxiliary information about the data, such as what units are used, may be stored with the data file. Generic utilities and application programs can access netCDF files and transform, combine, analyze, or display specified fields of the data. The development of such applications may lead to improved accessibility of data and improved reusability of software for array-oriented data management, analysis, and display.

For more information about NetCDF, just visit NetCDF User's Guide.

In this demo, the example NetCDF file is created from 3D volume data (lobster.dat). A simple application using Read_Volume and Write_netCDF allows to convert the volume data into NetCDF data.

The main user interface of this demo contains a file menu, several buttons and one slice. Ihe file menu, load_Channel# gives the option to load different NetCDF files for individual channels. The submenu "Unset Channel" disables the specified channel (1,2,3).

The small button:

• SU: show surf_plot of a specified chanel that you can select with the Channel_# buttons
• VO : Volume rendering (In this demo, we call it Vortex rendering)
• VE : Isosurface rendering (In this demo, we call it Vertex rendering)

The Big buttons:

• Crop : shows a crop interface to set i,j,k limits
• E_Vertex : Edit the selected channel Vertex object (Vertex viewer must be on).
• Volume : Show Volume calculation interface
• Channel#: Enable or disable channel#.

Slice

Set the slice position for 3D volume data.

User Macros

Two user macros are provided with this project:

• Axis
  creates an XYZ axis grid with labels based on mesh extents. It is a simplified Axis3D macro.
• my_crop
  extracts a subset of a structured field. It is a simplified crop macro.

Files

iac_proj/confocal/conf_macs.v contains the V definitions of the Axis and my_crop user macros.

iac_proj/confocal/conf_apps.v contains the V definitions of the ConfocalMicrocopyDemo demo applications.

Other Notes

This project does not contain any procedural code and hence does not require compiling.

Author

Steve Thorpe

Modifications

MA YingLiang
Manchester Visualization Centre

Contact

International AVS Centre
Manchester Visualization Centre
Manchester Computing
University of Manchester
Oxford Road
Manchester
United Kingdom
M13 9PL