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Opening a Dataset

To open a dataset select File >> Open... from the menu. This brings up the standard dialog for exploring your file system. When opening a series you may select any one file in the series and the program will detect all files in the same folder that have the same name prefix. The series is ordered according to the number after the file prefix. This number can be padded with zeros but it is not required. For example given a sequence of images named a0001.tif ... a0140.tif, opening the image a0097.tif will bring up the following message.

Opening a 2D Sequence

Hit Yes to open the entire sequence, No to open the single image, and Cancel to abort.

The program supports files in TIFF (Tagged Image File Format), RAW (binary), and LSM format. Currently the program only accepts greyscale images of 8 or 16 bit-depth. 12-bit greyscale is also allowed but each pixel must be padded to 16 bits (i.e. 4 unused bits). Floating point pixel formats are currently not supported.

TIP: Use the Ctrl+O key combination for easier opening.

RAW File Format

For RAW format only, you will need to know the dimensions and bit-depth of the dataset before loading the data. For 16 (or 12) bit greyscale data you will also need to know the byte order. A simpler way of setting this value is to knowing what type of machine the image was saved on. See also the image below.

Opening A RAW Image

TIP: For greyscale images the number of channels (Count) should be 1.

TIP: The header is almost always not present. Therefore leave this value as 0.

If the specified dimensions and bit-depth do not match the size of the file, a message will appear asking for confirmation.

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Send questions or comments to: alfredo.rodriguez@mssm.edu