Glossary

Image processing

Contrast and brightness

For monochrome images : it enables contrast and brightness enhancement. For 16 bits images, it uses a non-linear image processing algorithm, according to the DICOM standard. (Check the part 3 of the C.11 DICOM standard for more detailed information).

Transparency

Enables transparency. When mouse is moved toward the left, transparency will increase, where as a left movement will reduce the transparency.

Add a color table

Add a color table to grayscale images. Two color tables are available :

• a golden color table :

• pixel intensity (PI) min (0) = red
• PI from 0.25 to 0.50 = orange
• PI from 0.50 to 0.75 = yellow
• PI from 0.75 to 1.0 = white

• a multicolored table

• PI from 0 to 0.25 : blue,
• PI from 0.25 to 0.50 : green,
• PI from 0.50 to 0.75 : yellow,
• PI from 0.75 to 1.0 : red.

Moving image

The image is selected when a right-click is performed on the image. Then drag it with your mouse. It will be moved according to the mouse movements.

Scaling image

The image is selected when a right-click is performed on the image. Then drag it with your mouse. It will be scaled according to the mouse movements. When mouse is moved toward the bottom, the image size increases, whereas an upward movement decreases the size.

Refresh image parameters

• zoom factor is automatically calculated to use the maximum space possible according to the window size,
• contrast and brightness are reset to the default values included in the metadata dictionary of the current DICOM image (only for 2D images),
• images are redrawn so that the upper left corner of the image coincides with the upper left corner of the window. The displacement of the image on the screen is canceled

Link images

• When pressed in 2D view mode, images which belonged to the same DICOM dataset and are acquired in a similar orientation plane (two axial series for example) are automatically synchronized. If the images belong to different DICOM datasets, the user has to manually synchronize the images.
• When pressed in 3D view mode, image contrast and transparency changes are synchronized between all the views.

Choose the number of windows displayed

When pressed, the user can select the number of windows displayed, from 1x1 to 3x3 windows. The selection of the windows is performed with the mouse (see below).

Navigate through the DICOM volume

When pressed, a blue set of cross lines are displayed on the DICOM images. The intersection point corresponds to the actual position in the three views of the volume (sagittal, axial and coronal view).

When toggled, the blue cross lines are displayed. When unchecked, the blue cross lines are hidden but the user keeps the ability to navigate through the DICOM volume when is toggled.

Database management

Configure the database path

Creates or modifies the link to the database. The path to the database is stored for future use.

Edit the database (shortcut : F2).

Clean and repair the DICOMDIR

Typically, standard DICOM files are associated with a file named DICOMDIR in its root directory. The DICOMDIR file store paths to DICOM files on the media. The DICOMDIR is a DICOM Object holding a sequence of nodes, each having a type like PATIENT, STUDY, SERIES or IMAGE. Sometimes nodes are incomplete or corrupted. This function will restore some of the missing attributes according to the DICOM standard.

Anonymization

It is highly recommended to anonymize the data stored in the database to prevent loss of medical or confidential data. JIMBO offers a tool to remove personal information from the headers of images. This software goes through all the images metadata dictionary and proposes to replace personal data the most commonly associated with DICOM images.  By default, the following headers, if present, are deleted:  

• "0008 | 0080" = Institution name
• "0008 | 0081" = Institution address
• "0008 | 0090" = Referring Physician’s Name
• "0008 | 1040" = Institution department
• "0008 | 1050" = Performing Physicians’ name
• "0010 | 0010" = Patient’s name
• "0010 | 0020" = Patient ID
• "0010 | 0030" = Patient’s birth Date
• "0010 | 0040" = Patient’s Sex
• "0010 | 1010" = Patient’s Age
• "0010 | 1030" = Patient’s Weight
• "0008 | 1048" = Physicians of record
• "0008 | 1010" = Name of the station
• "0008 | 1070" = Operator name
• "0010 | 0020" = Patient Id number
• "0010 | 0040" = Patient Sex
• "0010 | 21c0" = Patient Pregnancy status
• "0018 | 1000" = Device serial number
• "0032 | 1032" = Requesting Physician

These items are highlighted in green in a full-sized table. The fourth column of the table can be edited to change the content of the DICOM header. Any changes will be highlighted in green in the table. The cell background stays painted in white if no change is made.

Load a directory in the database from existing files (USB keys, CD-ROM, DVD-ROM…)

When this icon is toggled, a dialog window enables to parse existing files stored in the computer. The user is invited to choose the repertory where the DICOM images are stored (USB key, CD-ROM…).

1. Often, this repertory is named “DICOM” or “IMAGES”.
2. If the DICOM images are stored in multiple directories, choose the repertory above. JIMBO will parse through the directories and will select the DICOM images.
3. If the loading operation failed, manually copy all the DICOM images in a single repertory (eg /DICOM or /IMAGES) and and try the task again.

Load a CD-ROM in the database

It is the easiest way to load DICOM images in the database. When a CD-ROM is inserted, and if it contains a DICOMDIR, the DICOM images will be automatically downloaded and stored in the database when the user press this icon. Before doing this action, the user must wait for the CD-ROM is recognized by the operating system (Windows or Linux), otherwise, JIMBO will tell that no DICOM image is present in the CD-ROM.

Exportation tool

When pressed, enables to :

1. export DICOM images. The user select a line in the database the press this icon. A dialog window will ask to choose a location on the disk and write a name for the new directory. The DICOMDIR and the corresponding DICOM images will be uploaded in that new location.
2. export the whole database to a new location chosen by the user. The new location can be an other directory in the computer or in a This task can be time consuming, depending on the size of the data. The whole database will be exported to the new location and the data in the database will be updates to match the new file path.

Show the database

When this icon is selected, the current windows are hidden and the database is displayed (see use the database for more information).

Help

When pressed, a file containing this document is displayed.

Tools for 3D navigation

CA - CP navigation

When checked, the sagital, coronal and axial view of the volume are displayed according to CA-CP orientation (CA = anterior commissure, CP = posterior commissure). The axial view is parallel to the CA-CP line and its vector normal is parallel to the CA - interhemispheric scissure line. To be effective, CA/CP/VB/VU CA must have been previously selected. The coordinates of these points are stored for future use and is displayed in a table named “Coordinates, world and Leksell reference planes”.

Free rotation of the volume (oblique reslicing)

When this icon is checked, the oblique reslicing mode is activated. This mode is activated when the right mouse button is pressed. See “DICOM volume reslicing for more informations”.

The user can manually unchecked this icon to go back to the initial view of the volume.

Locate depth electrodes (advanced users)

When checked, shows the entry point and the target point of surgical devices (eg: depth electrodes). On the left side, the points are colored in red (bright red for the target point, pale red for the entry point). On the right side, the points are colored in green (bright green for the target, pale green for the entry point). See “how to set target and entry point” for more information. This function is deactivated when an oblique reslicing is performed. This function is intended to be used when CA-CP points are set. See “Set CA CP reference points” for more information.

MMR registration of volumetric data

When toggled, a Multi-modal 3D image registration algorithm is performed using mutual information maximization on both DICOM dataset. The user can change the number of random points used by the function. For MRI/TDM registration, 0.5 value provides often accurate results. For MRI/TEP-Scan registration, the user should select “use all pixels”.

3D viewing mode

When checked, it informs the user that the 3D mode is activated.

2D viewing mode

When checked, it informs the user that the 2D mode is activated.

3D Rendering mode

When checked, it activates the 3D rendering mode. Several options are available. See “3D rendering tools” for more information.

Add overlay

When this icon is checked, a table is displayed. Each row displays a registred volume dataset. When a specific row is double-clicked, the chosen volume dataset is displayed in the foreground with a slight transparency effect.

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