Job configurations consist of a series of input fields and control elements that configure the job. Most of them are standard UI tools like buttons and checkboxes, and we assume you are familiar with their use. However, there are a number of specialities, and we will introduce them in this section.
The visibility of many input fields in rapidSTORM is dependent on previous choices, i.e. the value of fields that are displayed above the current field. Therefore, changes in text fields are not immediately committed while you type. While a field is not committed, its values do not take effect, and its background is red. You can commit a textfield by pressing Enter or switching the keyboard focus away from the field, e.g. with the Tab key or clicking another field.
Text fields in rapidSTORM are often part of a matrix. You can recognize matrices by the presence of multiple text fields with one description. Next to a matrix field, a button with a chain is shown.
The chain button is used to "chain" the matrix elements, that is to change all elements at once (chained) or individually (unchained). When text fields are chained, entering text in one of the fields immediately changes the text in all fields. When text fields are unchained, each field is changed and committed individually. Leading unchained text fields in a matrix do not commit their values when they lose focus; only the last text field in the matrix behaves in this way.
Some values in rapidSTORM are optional, that is, they can have no value at all. These fields have a checkbox in front of them. The checkbox controls the presence of a value, and the text field is not displayed while the checkbox is not checked. When you check the checkbox, the text field will be uncommitted and has to be committed in the usual way to take effect.
When a text field in rapidSTORM requires a file name, you can enter the file name directly, select it interactively with a dialog by clicking the Select button next to the field, or by dragging & dropping the file on the input field.
Localization jobs and replay jobs organize their output in an output options tree. This tree is displayed with a tree element on the left, which shows the structure of the tree and allows selecting a single node, and the node detail field, which shows the detailed options for the tree node selected on the left-hand side.
Each node in the output tree represents an output module, which will perform some action with or display information about the output. Some of the output modules such as the Expression filter modify their input and can have subordinate output modules. The subordinate output modules will act on the localizations that were modified by their parent output modules.
The first, root node (called "dSTORM engine output") symbolizes the output of the the section called “dSTORM engine”. Each module connected to it receives all localizations found by the engine without filtering or processing.
For an example, consider the tree shown in the graphic: The first Localizations file, Count localizations, Display progress, Filter localizations and Average images receive the unmodified output from the the section called “dSTORM engine”. The localizations received by the second Localizations file and for Image display are those modified by the Filter localizations module.
Clicking on an output module in the tree view shows this module's configuration in the right part of the display. Each module has specific configuration options, which are documented together with the module's description in the Output options chapter. You can manage the suboutputs by the following standard control elements: