Use the Files browser to import laser log files.

1. Click Import Log to prompt the file browser window.
2. Select the log file you want to use and then click Open. You must have already imported the associated mass spec data before importing the laser log.
3. In the sync window, you can:
   • Adjust the time overlap between the laser log and the mass spec data. To do this, drag the laser data (the green trace) by holding down the Shift key and clicking and dragging the trace.
   • Zoom the x axis using the mouse scroll button.
   • Change the x axis extent by clicking and dragging the graph.
   • Use the Laser Offset variable display at the bottom left to set an exact offset, if known for your system. The up/down arrows move in 1 s increments, but you can manually type in the offset for finer control.
   • The Duration field allows you to define the search window for an overlap. For example, if your mass spec data spans a time period of one hour, using a value of 2 for Duration will look for an overlap with the laser data up to one hour before the start of the mass spec data and one hour after the mass spec data ends. This is useful if your datasets are initially quite far apart in time. Increase this value to help with auto-syncing your data.
4. Once you're happy with the offset, click the Done button to finish the import.

If you want to re-sync a laser log file, select the log file in the list of imported laser log files, and click the Sync button.

The Time Series browser allows you to view and modify the display attributes of the different channels. It also allows you to add and delete selections, as well as to modify the duration of existing selections.

This browser has two main components: the Settings panel and the Time Series window. You can view the Settings panel by clicking the Settings Wheel icon found in the top-left corner of the Time Series window.

The Settings panel is divided in three parts: Channels control, Group view and Selections display panes. Each pane can be hidden or displayed at any time by clicking its corresponding toggle button at the bottom of the Settings panel.

• Channels control. This pane allows you to display and/or hide channels in the Time Series window. It also allows you to change the display attributes for each channel such as scale and style.

  Display a channel:

  1. Select a channel from the channel list.
  2. Click any of the double arrow symbols found in the Axis control box. Clicking on the left double arrow plots the selected channel on the left y-axis of the Time Series graph. Clicking on the right double arrow plots the selected channel on the right y-axis.

  Change the vertical scale:

  1. Select a channel from the channel list.
  2. Click any of the scale buttons found in the Scale control box to modify the scale of the y-axis of the selected channel on the Time Series window:
     • Auto autoscales the y-axis of the selected channel to fit the plotted data.
     • Visible resizes the y-axis of the selected channel to fit the extent of the data displayed in the x-axis.
     • Log displays the y-axis with a base-10 logarithmic scale.
     • Manual allows you to manually supply the y-axis minimum and/or maximum limits of the selected channel.
     • In zooms in the y-axis of the selected channel.
     • Out zooms out the y-axis of the selected channel.

  Modify the style:

  1. Select a channel from the channel list.
  2. Click any of the options found in the Style control box to customize the style attributes of the selected channel.
     • Clicking on the Pencil icon brings up the Color panel. This panel offers several color picker interfaces such as Color Wheel, Color Sliders, Color Palettes, Image Palettes and Crayons. How you choose a line color for the selected channel depends on the colour picker you select.
     • Use the Style button to change the line style. Channels can be drawn as solid, dashed, dotted and dash-dot lines.
     • The Weight button allows you to change the line thickness.

You can create selections from the Samples browser.

1. In any of the samples list, select the samples from which you would like to create selections.


Tip: You can also search for selections using the Search... input field in the top right of the window. This search tool is case-sensitive and (for advanced users) does not use wildcards such as | or *.


2. Click the Create selection from sample button.
3. In the Create Selections window, you can choose to crop the start and end times and select which group you would like to add the selection(s) to.

If the selection group you'd like to use doesn't appear in the list, you can add a new selection group by typing in a new name (e.g. "Output_1"). If the selection group already exists, and you'd like to overwrite the existing selections with the selections you're about to add, check the Replace existing checkbox.

Remember: You can check the messages logged during sample selection creation by going to the Messages browser. There you can find information on the number of selections added, the group to which these selections were added to, the start and end crop times used, and the total number of selections in a group after creating the selections. This information can be useful when trying to re-create selections.

The Selection browser allows you to edit certain properties of all the selections within a selection group or of any individual sample selection at a time.

The properties that can be edited include:

• Name: This field displays the name of a selection group or a sample selection. You can change the name of a individual selection or of an Unknown group, but you cannot alter the name of Baseline or Reference Material groups.
• Duration: This will adjust the end time of all selections within a selection group or of a single selection. For example, to change the duration of a group of selections click on the name of the group and then type 30 s into the Duration (s) field. This will adjust the end time of all selections within that specific group to be 30 s after the start time.
• Internal element: This field displays the internal standard element used to standardise that particular selection group or sample selection.
• Internal units: This field displays the units in which the value of the internal element is given.
• Internal value: This field displays the abundance of the internal element in a sample selection or all the selections within a group.
• Start time: This field is only displayed if a single sample selection has been selected. This value can be manually modified to change the start time of the selection. Changing this value will change the Duration value accordingly.
• End time: This field is only displayed if a single sample selection has been selected. This value can be manually modified to change the end time of the selection. Changing this value will change the Duration value accordingly.
• Comment: You can provide more detailed comments about a sample selection by typing into this field.

You can add properties to a selection by clicking the plus circle at the bottom of the properties. This will add a new property with the name "My New Property". You can edit the name of this property and the value associated with it by double clicking in the title or value cells. You can remove any of the non-default properties for a selection by clicking the dash button to the right of the property. However, you cannot remove default properties.

The Selection browser allows you to move, copy or delete selections.

Selections can be moved between groups, or copied to another group using the Move and Copy buttons at the top right. You can also delete selections by clicking the Delete button.

You can also drag and drop selections between the groups by selecting them in the list and dragging them to a new group.

The Reference Materials browser shows the values and metadata associated with the available Reference Materials files.

Reference Material (RM) files are loaded at start up. To view or modify the folder iolite looks for RM files at start up go to iolite 4 > Preferences or press Ctrl + , (Cmd + , on Mac) and select the Paths tab. The Reference Materials item will show the current location of RM files.

RM data are stored in text files in JSON format (for more information about this file format, click here). Each RM file contains some metadata, such as the matrix type (e.g. glass, zircon etc), the data source (e.g. GEOREM), and a list of values in an array called "Results". See the default RM files included with iolite 4 for examples on how to create new files.

The Reference Materials browser is divided into two main parts: a list of RM that are grouped by matrix types on the left and the information area on the right. You can expand each of the listed group types by clicking the expand arrow. Clicking on any of the RM will display its information in the right-side window.

The right-side window has two tabs:

• Meta-data: This tab displays information on the matrix type, data source, etc.
• Data: This tab displays each of the values within the reference file.

The default RM files included with iolite cannot be altered, but they can be copied and edited under a new name. You can edit any of the values by clicking on them. You can remove a value by clicking the dash button to the right of the value. You can add a new value by clicking the plus button at the bottom of the list of values. You can Copy RMs using the Copy button at the top right. Non-default RM files can be Renamed or Deleted using the Rename and Delete buttons.

The DRS browser allows you to create a new custom DRS or open and existing one. Custom DRS are written using Python language.

Create a new custom DRS

1. Click the Plus icon at the top of the DRS list.
2. Set name and location for the new DRS file in the dialog that appears.
3. Click Save. This saves a .py file template that you can use as a starting point. This template includes settings and instructions that you need to develop a custom DRS.

Open an existing custom DRS

1. Click the Open File button at the top of the DRS list.
2. In the Open dialog box, browse to the file that you want to open.
3. Click Open

The Export module is used to download your results for use outside iolite. Exported data files may include input and output channels, as well as metadata.

To export your results:

1. Go to the Export File tab.
2. Select your export options.
3. Click the Export button at the top right of the panel and then you will be prompted to save the file.

The available export options are:

• Export type: This option lets you choose to export your results as 'Stats' or 'Time Series'. Choose Stats to export the data as a statistics table and/or Time Series to export the results for every data point of the time-series.
• Format: Select Excel to export the results as a Microsoft Excel spreadsheet file and/or CSV to export the results to a comma separated value (csv) file.
  The Excel export file contains a spreadsheet for each of the following information:
  • Metadata. Information gathered by iolite during sample import and laser log file import.
  • DRS Settings. The DRS settings used for data reduction.
  • Reference Material Values. The standard values used for calibration.
  • Data. The results of the data reduction process.
  • Processing Log. The messages logged by iolite during data processing.
  
  The CSV export file contains only the results of the data reduction process.
• Selection groups: Use this field to select which selection groups should be included in the report.
• Channels: Use this field to select which channels to export.
• Report: This option allows you to choose what to report in the export file when using Stats as export type. You have several options to choose from:
  • Mean
  • Median
  • 2 Standard deviation
  • 2 Standard error
  • Number of points
  • Report results belo LOD as "belowLOD"
  • Include QAQC results
  • Include messages log
  • Limits of detection
• Sort: Defines how the selections will be sorted in the exported file. For example, 'by group then time' will sort each group of selections by time, keeping them in their groups. The option 'by time' will sort the selections according to their start times, irrespective of their selection group. The option 'by label then time' will sort the selections according to the selection label, irrespective of their groups.