Data Loading and Saving

Data Formats:

The following data formats are supported for loading and saving image and segmentation data:

1. NIfTI (Neuroimaging Informatics Technology Initiative)
2. VTI (VTK'S XML Image Data format)
3. Single multipage TIFF file (loading only)
4. Stack of TIFFs

When loading data as a stack of TIFFs, it is assumed that all files in the directory belong to the stack, and that the file names are in alphanumeric order (e.g. image_001.tif, image_002.tif, etc.).

Image Data Loading:

To load image data in NIfTI, VTI, or multipage TIFF format select File->Open Image File... and choose the desired file. To load image data in stack of TIFFs format, select File->Open Image Stack... and choose a single file from the directory in which the image stack is stored (the other files will be loaded automatically).

After loading data, the 2D slice view on the right will display the current slice.

Creating an Initial Segmentation:

To generate an initial segmentation, select Analyze->Segment Volume.... The segmentation method currently consists of an Otsu thresholding followed by morphological followed by calculating the connected components.

Once the initial segmentation is generated, the 3D view on the left will display surfaces of the segmentations, and the 2D slice view will show 2D overlays and outlines of the segmented regions on the current slice.

Segmentation Loading:

To load segmentation data in NIfTI, VTI, or multipage TIFF format select File->Open Segmentation File... and choose the desired file. To load segmentation data in stack of TIFFs format, select File->Open Segmentation Stack... and choose a single file from the directory in which the segmentation stack is stored (the other files will be loaded automatically).

Image Data Saving:

To save the image (useful for file format conversion) select File->Save Image Data.... The format will be based on the file extension provided (.nii, .vti, or .tif).

Segmentation Saving:

To overwrite the most recently loaded or saved segmentation file, select File->Save Segmentation Data. To save as a new segmentation file, select File->Save Segmentation Data As.... The format will be based on the file extension provided (.nii, .vti, or .tif).