# XL Formats

The Perkin-Elmer Elan 'XL' format (*.xl) is generated by control software of ICP-MS instruments from Perkin-Elmer such as Elan 6x00 or Elan DRC-e.

When using this format in LA-iMageS, each dataset should be placed in a folder containing the *.xl files corresponding to each data line taken by the ICP-MS instrument. The following listing shows an example of a valid XL file.

    Intensity Vs Time, Counts Per Second
    Time in Seconds ,SeO96,SO48,C13
    0.,0.,290.0050460878,1250.093757031

    0.,0.,280.00470407903,1230.090780699

    0.,0.,630.0238149002,1150.079355475

    0.,0.,2010.2424352377,1230.090780699

The name of the folder will be used as the dataset's name. Each line file must contain a number that indicates the order in which each line has been acquired by the ICP-MS instrument. For example, if you have a dataset with 10 lines, a valid set of names can be: line 1.xl, line 2.xl, line 3.xl, line 4.xl, line 5.xl, line 6.xl, line 7.xl, line 8.xl, line 9.xl and line 10.xl.

Additionally, the dataset folder may contain two configuration files: parameters.conf and positions.txt.

## The parameters.conf file

The parameters.conf file is used to store the ICP-MS data acquisition parameters:

- Standard: the standard element in the dataset. The other elements will be normalized using this element as standard. Internal standard is used to normalize the results and to overcome the instrumental oscillation. Users must choose a specific element to be monitored, for example, a known matrix element in the sample or those intentionally added by user. The chosen element should minimize the variability of the ablation process, which can be caused by local differences in tissue thickness and different interaction between the laser and the sample surface. Thus, it will be possible to show that observed signal corresponds to an elemental concentration in a specific local.
- Ablation speed: speed set by the user in the laser operational mode as continuous firing. This parameter relates to the spot size, which is determined by the laser beam diameter, and frequency, which corresponds to repetition rate of laser. Usually, a lower value of ablation speed than spot size is used.
- Acquisition time: refers to the time needed by the acquisition of one point for all elements monitored by the ICP-MS. This parameter is intrinsically linked to ICP-MS parameters, such as the number of isotopes monitored, sweeps, number of replicates and dwell (or residence) time. The acquisition time should not be higher than 1.0 s, since that the elemental distribution information would be lost.
- Space interval: is the distance among the center of two lines. The lowest space interval results in the highest image resolution.

This file is optional and it is used by the Load Data operation in order to automatically load the acquisition parameters. If this file is not present in the dataset's directory, user must explicitly introduce them. The following listing shows an example of a valid parameters.conf file.

    standard=C13
    ablation.speed=0.06
    acquisition.time=0.324
    space.interval=0.12

## The positions.txt file

The positions.txt file is used to store the physical position of each line in the instrument during the ablation process. The following listing shows an example of a valid positions.txt file.

    LINE
    16.5460,31.3610,4.4210
    17.5140,31.3610,4.4210
    LINE
    16.1270,31.2410,4.4210
    17.9880,31.2410,4.4110
    LINE
    15.9720,31.1210,4.4150
    18.7480,31.1210,4.3550
    LINE
    15.6940,31.0010,4.4150
    19.0860,31.0010,4.3250

This format consists in blocks that starts with by keyword LINE followed by at least two lines of three comma-separated numbers (X, Y, Z). The first and last lines of numbers represent the initial and final positions of the corresponding line. There must be the same number of LINE blocks and *.xl files.

This file is optional and it is used by the LA-iMageS software in order to read line's positions and determine whether they are horizontal or vertical: if each line has the same X position and Y initial and final positions are different, it means that it is vertical; otherwise, if each line has the same Y position and X initial and final positions are different, it means that it is horizontal. If this file is not present in the dataset's directory, then La-iMageS will consider that lines are horizontal and will automatically generate its positions based on the acquisition parameters.