Images Preferences

Many common image file formats (eg. .tif, .gif, .jpg, .png etc...) are supported via the OSX graphics importers.

Plaque Simulator creates both a 32 bit color and an 8 bit monochrome version of each image file opened and provides various image enhancement capabilities that may prove helpful in identifying anatomic landmarks and differentiating tumor from normal tissue. You can customize some of Plaque Simulator's image related startup behaviors in this preference pane.

In the Rulers control group you can customize the behavior of ruler automatic initialization when calibrating MPR (e.g. CT and MRI reconstructions) and ultrasound images. You can establish independent or common preference settings for MPR and US images, and for horizontal and vertical rulers within each image context. Automatic ruler initialization searches images imported from external applications such as OsiriX and Horus for green hued rulers with tick marks. You can customize the ruler hue to something other than green here. Rulers need to be a color that stands out distinctly against the grey shades of CT, MRI and b-scan images, so bright green works well and is often used for rulers superimposed on monochrome medical images.

The default settings are those that Eye Physics has found work well for .jpg images exported from OsiriX that are roughly 1000 ± 500 pixels in width and height. Auto initialization works by creating an 8-bit monochrome equivalent of the image being calibrated. All pixels in the original image that have a greenish hue (HSL color space) are converted to black pixels in the monochrome version according to the criteria set here for hue angle tolerance, saturation and lightness range. All non-greenish hued pixels become white. You can view the resulting monochrome image in the Image window using the provided footer button. The monochrome image is then searched for its longest horizontal and vertical runs of contiguous black pixels. These runs are then searched for tick mark patterns and a histogram of the distances between tick marks is created. If a histogram bin exists with multiple similar tick mark separations then that information is used to propose an initialization and calibration distance for the ruler.

In the MPR meta-data control group you can customize the default preference settings of parameters used in the MPR window for managing a series of CT (or MR) images from which planar and spheroidal surfaces can be reconstructed and used directly or captured as PSImages for additional processing in the Image window. This technology will be "officially" introduced in version 7 of Plaque Simulator but you can preview it beginning with version 6.8.6. PS version 6.8.6 requires a folder named DCMTK that contains a series of uncompressed HFS, axial, 16-bit MONOCHROME, little endian transfer syntax UID DICOM images that have been converted to Dicom Toolkit DCMTK's .xml file format. Slice thickness should be <= 1 mm (e.g. CT with 0.5 or 0.625 mm slice thickness are commonly available).

Optionally, you can also use OsiriX to export images in Raw.nnn file format along with a file containing the DICOM meta-data of the first slice in .xml format as a file named "PatientName.xml", all located in a folder named "RAW".

In the Customizable pseudo color palette control group you can adjust the pseudo colors that are used when mapping spheroidal surface reconstructions on retinal diagrams. The default color palette is designed to highlight the tumor base using shades of brown to assist in mapping the tumor base.

The PSImage captures control group includes the settings used by the MPR window's auto capture feature which creates the six planar reconstructions used by the Images window for fine-tuning the eye model.

In the Annotations control group you can customize the appearance of annotations and the display time of the coronal thumbnail that appears when adjusting the displayed slice.


Either a DCMTK or RAW folder can be placed in the patient folder along with any other images. If present, a "DCMTK" or "RAW" folder will be parsed when dragging and dropping the patient folder on the PS Images window.