Reading Image Files

To read in most image files, use Read Files(RGB) menu. Choose the first of a series of files, and all the following files are automatically read in.

File Format

DeltaViewer can read files of formats supported by QuickTime Graphics Importer, which include, in particular, the following types.

.tif (.tiff)
Standard image format
Photoshop image file (versions 2.5 and 3.0)
.pct (.pict)
Macintosh QuickDraw PICT format
Windows bitmap image
TARGA bitmap image
Silicon Graphics
Silicon Graphics image
PNG image
.jpg (.jpeg)
JPEG compressed image
JPEG 2000 compressed image
GIF bitmap image

File Name

In order for a sequence of files to be automatically read, the file names must follow the following rule.

File Name: <string1><number><string2>.<extension>
Example: cup0.jpg

Here, <string1> is some character string, <string2> is some character string not containing numerals. They can contain symbols, and one or both of them may be empty. The <number> part may be simply 0, 1, 2, ..., 9, 10, 11, ..., or may have leading 0's as in 000, 001, 002, ... They do not necessarily have to start from 0.

Missing Slices

Serial sections from optical and electron microscopes often contain missing slices and/or "bad" slices, which result in missing images in a sequence. When DeltaViewer reads in image files, it automatically skips non-existing files in the sequence. DeltaViewer can later interpolate such missing images from the ones in front and behind.

Reading Color Components

In some situations like when data from confocal laser microscope scanned with different wavelengths are saved separately, these data sets must be read as different color components and overlaid together.

To do it, first read in the files of red component using Read Files(Red) menu. When all the files are read and SectionView window appears, use Read Files(Green) menu to read in and overlay the files of green component; and similarly for blue component if it exists.

The component files may be either grayscale or single-component color images. You can even read red-component color files, for instance, as green component.

Reading Raw Data

Sometimes a set of three-dimensional density data is contained in a single file. To read such a file, use Read Raw Data menu. Of course you need to know the internal format of the data. A text file with information on the data format is often found in the same folder as the raw data; look for one.

After choosing the raw data file, a dialog appears. Type in the following information and press OK.

Header length in bytes (usually zero)

Width, height, and depth of image in pixels

Whether density is stored as 8 bits, 12 bits, or 16 bits

If 12 bits or 16 bits, whether the principal part is upper byte or lower byte

The OK button is invalid if the total length of data computed from the supplied information exceeds that of the actual file.

Saving Image Data

If you choose Save As menu while SectionView is active, the rectangular part of the image bounded by yellow lines are saved as sequential image files. If the image has been transformed using Scale Images, Flip Images, Align Images, Negate Color, the transformed images are written to files.

In the Save dialog, choose format and name of the first file. Choosing a file format from the popup menu automatically changes the file name extension to an appropriate one; and typing in a file name extension also sets the popup selection accordingly.

Opening 3DView File

Use Open 3DView File menu to open files previously saved by DeltaViewer in the 3DView. Note that a file of very large size can take tens of seconds to open.

Saving 3DView File

Choose Save As menu while a 3DView window is active, and the 3D image shown in the window is saved as a disk file.