Importing the First Image Volume using Customization

The first image volume has the following special properties:

• No other images can be displayed until the first image volume has been loaded or imported
• All subsequent image volumes must have the same dimensions as the first image volume and will be discarded if they do not
• Loading or importing a new first image volume will cause all other images to be discarded if they do not match the dimensions of the newly loaded or imported first image volume
• Only the first image volume can be modified or saved

Files in the Analyze and MINC Image formats should be loaded rather than imported. Several file types can be imported directly without the need for customization.

• by loading the images (8 or 16 bit) as raw images, specifying relevant offsets, dimensions and voxel sizes
• by writing custom Java code to convert the images into a format that MultiTracer can import

To import the first volume image as raw images:

• From the main MultiTracer window "File" menu, choose "Custom Import First Volume ..."
• Select the file that you want to import from the "Open" dialog box. If the file is not in the current directory, the popup menu in the upper left of the dialog box will let you move up the directory tree, or you can double click on a subdirectory icon to move down the directory tree.
• Once the file is selected, click the "Open" button in the dialog box
• In the "Import" dialog box, set the type of image (8-bit, 16-bit signed, 16-bit unsigned)
• Set the width (x-dimension) of the imported volume in voxels and the corresponding voxel width
• Set the height (y-dimension) of the imported volume in voxels and the corresponding voxel heights
• Set the number of bytes in the file to skip before loading the first plane of data
• Set the number of images (z-dimension) of the imported volume in voxels and the corresponding voxel thickness (slice thickness plus any interslice gap)
• Set the number of bytes to skip between planes
• To invert black and white, check the "White is zero" box
• To load data stored in little-endian order (e.g., PC's, DEC alphas), check the "Little-Endian Byte Order" box
• Click the "OK" button
• Large files may take several seconds to load
• Once the file is loaded, the image should appear in the display region. If no prior image has been loaded, MultiTracer will automatically take you to a plane in the middle of the image and will adjust the intensity of the display to a (usually) reasonable value. If the display appears black, this may reflect a problem with the automatic intensity adjustment, and you may need to set the intensity manually.

To import the first volume image using custom written Java code:

• A Java programmer needs to write custom import code and provide you with the compiled custom class file
• From the main MultiTracer window "File" menu, choose "Set Custom Import Class ..."
• Select the compiled custom class that was provided to you using the "Open" dialog
• From the main MultiTracer window "File" menu, choose "Custom Import First Volume Using [YourCustomClass] ..."
• Select the file to import and follow any instructions specific to the custom import class that you are using
• You only need to set the custom import class once. The selection will remain in effect whenever you use the "Custom Import First Volume Using [YourCustomClass] ..." or the "Custom Import Volume Number.." menus until you choose a new custom import class or quit MultiTracer.

If you have already loaded or imported a file and choose to import a new first image volume with different dimensions, any tracings of structures will be discarded (you will be given a opportunity to save them first). Nonetheless, it is always a good idea to save your traces before you import a new image.

If you have previously loaded or imported a file and choose to import a new first image volume with the same dimensions, you will be given the option to discard or to retain any existing traces.

File importing in MultiTracer relies on public domain Java classes in Wayne Rasband's ImageJ 1.29 program. If you want to help support importing of additional file formats into future versions of MultiTracer, please consider contributing code to Wayne Rasband for incorporation into ImageJ.

Modified: April 22, 2003