Handling Images

Loading Images

As well as being able to import images in many popular medical image formats, Jim currently recognises the following image file formats:

  • NIFTI format (both NIFTI-1 and NIFTI-2) from the Neuroimaging Informatics Technology Initiative consortium. All pixel data types are supported except 64-bit unsigned int and 128-bit floats. Both two-file (.hdr/.img) and one-file (.nii) formats are supported.

    • Images compressed using gzip (.gz) may be loaded directly, and will be decompressed as they are loaded.

    • Both big-endian (Sparc/SGI format) and little-endian (Windows/Linux PC format) images can be read.

  • AnalyzeTM (not AVWTM) format from the Mayo Clinic. Images at 1 bit per pixel (binary), 8 bits per pixel (unsigned byte), 16 bits per pixel (signed short), 32 bits per pixel (signed integer), floating point (32 bits), double (64 bits), complex (2×32-bit float interleaved) and colour (3×8-bit values, ordered by colour plane) are all supported.

    • Both big-endian (Sparc/SGI format) and little-endian (Windows/Linux PC format) Analyze images can be read.

    • Images compressed using gzip (.gz) may be loaded directly, and will be decompressed as they are loaded.

  • DICOM format. Although you can directly load individual DICOM images, this is not recommended, since each DICOM file typically only contains a single image slice. You should instead use the Image Converter to compile the images into multi-slice datasets. However, you may find it useful to load DICOM images directly if you work with the newer multi-slice/multi-frame DICOM images.

  • University of North Carolina (UNC) libim format. Integer images stored at 8 or 16 bits per pixel, floating point images (32 or 64 bits per pixel), complex (2×32-bit float) and colour packed (R,G,B,alpha) are all supported.

    This data format was modified to include image information fields by David Plummer, Medical Physics and Bioengineering, University College London.

If you need to load images in other formats, please mail to E-mail to contact Xinapse Systems support to discuss your requirements.

When you download and install Jim you may also have chosen to download some example images so that you can get started with Jim. These example images are in the UNC format.

To load an image in one of these formats, you can:

  • Select Load ... from File menu. The file load menu item.
    A File Chooser dialog will now appear, allowing you to select an image file of one of the recognised types. You may select a file filter, so that only UNC, AnalyzeTM, NIFTI or DICOM images are shown in the list of selectable files. There are some general instructions on using a File Chooser. Select a file from the list, or type in the file name of an image that you know exists. The image will now be loaded, or an error message will appear telling about the problem that prevented the image from loading.

  • Click on the file loader icon Press this icon to to load an image.
    A File Chooser dialog will now appear, as above.

  • Type in the full path to the image in the image source text box Text box showing the source of an image.

  • Drag and drop an image file onto the image display area. For AnalyzeTM images, you must drop the ".hdr" file.
    Note: drag and drop may not be supported for your operating system.

  • When you have loaded an image, it will be listed in the Recent Images, which is accessed for the File menu:

The recent images menu

You can also access the Recent Images by pressing and holding down the right mouse button on any Image Selection panel, like this:

Floating recent images menu

You can configure how many recent images are retained in the Recent Images menu using the Preferences dialog.

After the image has loaded, it will be displayed and the image source text box (near the top of the Image Display frame) will show the source of the loaded image.

Text field showing the image name

If you want to load another image of a similar name, you can simply edit this text to name of the new image, and then press the Return key. If you have correctly typed in the name of an image, then this will now be loaded.

If you do not have images in UNC, AnalyzeTM or NIFTI format, you can load images using the Import facility.

Launching a File Manager

You can browse through folders and files using a regular File Manager which can conveniently be launched from within Jim by selecting "File Manager ..." from the "File" menu:

Launching a file manager from within Jim

When launched, the folder shown will be that of the image that was last loaded into Jim's display. Note: this feature may not be available on all computer platforms. If it is not available, the menu item to launch a file manager will not be present.