Saving a Dataset as Gate Images

In some cases, it might be desirable to save the current dataset, either to change its file format, or to preserve the result of a series of operations. For instance, accumulated dataset, or datasets with rejected gates, background-subtracted datasets, etc.

Two options are currently offered: One is specific to AlliGator (and is bound to evolve over time) but should be easily readable by other software (see the corresponding manual page), and the other consists in exporting the different gates as TIFF images.

 AlliGator currently offers the possibility to export the gate images as individual TIFF images, adding a metadata text file containing basic information on how to interpret these images, and on the data source.

This is achieved with the File>>Save>>Dataset>>Save as TIFF Gate Image Folder menu item:

Some parameters need to specified in the Settings>>Miscellaneous tab:

The first parameter to define is the bitness B of the image files: 8 or 16 bits. The respective maximum value for 8- and 16-bit images are R = 2^8-1 = 255 and R = 2^16-1 = 65,535 respectively.

Next, a Min Value m and a Max Value M need to be define to convert the original gate pixel values P_o into exported TIFF image values P_e, according to the following formula (***):

P_e = int(R*(P_o - m)/(M-m))

where int indicates the integer part (floor function).

Finally, a dialog window is opened at the beginning to specify name format, compression and whether or not to save a metadata text file:

• • The File Name will be common to all images (and metadata file) and will be followed by an image number defined by the File Number Format string (see Context Help window shown below for information on this string, but the default format should be appropriate for most cases). It is recommended (but not mandatory) to add a space or underscore character right after the name in order to separate the name from the index.

• • The Start Index control specifies the index of the first file, each subsequent file being increment by 1.

  • The Save Metadata File checkbox is self-explanatory. This text file is saved in the same folder as the TIFF images, and is used by AlliGator to load the necessary information to make sense of the images.

  • The Compress Image checkbox specifies whether or not the images are compressed. While compression (using the zip algorithm) is generally very efficient for images that contains sparse data, it might not be supported by all software. 

The next File Dialog window will allow selecting the folder in which to save all these files. If the files already exist, they will be overwritten.

Try to create one folder per dataset.

These files can be reopened in AlliGator as any other gate image folder.