The DNS Analysis Creator Macro creates an *.ijx analysis configuration file that ImageJ can use to order, group, and process images in sets described in the DNS Macro Example Overview.

 

 

The analysis configuration file is a comma separated value (.csv) text file, with an .ijx extension. The first line of this file must contain a column header(s). For example: Filename, Channel.

 

The valid column headers for the .ijx file are:

 

Filename: It must be the first field, and must be the fully qualified path to the file, this is, including the full path to it. It can not be empty. For example, c:\image data\img004.jpg.

 

Channel: (Optional) If present, it must be the second field. It can not be empty. For example, it can be: green. The channels can be any name you like but must repeat for different wells, fields of view etc..

 

Well: (Optional) If present, it must be the third field. It can not be empty. The format is one or two letters, in the range a..z, A..Z, followed by at most four digits in the range 0..9. For example, it can be B07.

 

FOV_row: (Optional) This is the number of the row for the field of view or tile/stitch position in a montage image. Fields of view are reassembled into a grid according to your specifications. If present, it must be the fourth field if "wells" are present, or the third field if "wells" are not present. It can not be empty. It must be an integer number, denoting the row of the field of view, starting at 0 (zero). For example, 0

 

FOV_col: (Optional) This is the number of the column for the field of view or tile/stitch position in a montage image. Fields of view are reassembled into a grid according to your specifications. If present, it must be the fifth field if wells are present, or the fourth field if "wells" are not present. It can not be empty. If FOV_row column is present, this column must be present, too. It must be an integer number, denoting the column of the field of view, starting at 0 (zero). For example, 2

 

These are examples of headers:

Filename

Filename,Channel

Filename,Channel,Well

Filename,Channel,FOV_row,FOV_col

Filename,Channel,Well,FOV_row,FOV_col

 

Additional Notes:

a.There must be at least one column for the image file name with full path. If subsequent columns are present, all intervening columns must be also present. For example, if you choose Filename and Well you must also have a column for Channel present, resulting in Filename,Channel,Well.

b.Header keywords are case-sensitive.

c.There are no default values for the fields. This means that two consecutive delimiters are not allowed.

 

 

How to create an .lJX file

 

The analysis configuration file (*.IJX file) may be created by:

 

• Using the DNS Analysis Creator Macro

• Using the DNS IJX writer in Excel utilizing Excel based macros  

• Manually editing the .IJX file in ImageJ or Excel

 

 

In the next section, we will complete the Creating a .ijx Analysis Configuration File section of the tutorial