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ROI CONTROLS Panel & ROI DISPLAY Figure
The ROI Controls and ROI Display Figure work together to depict and interact with the hierarchy of ROIs currently cached by ScanImage. The tabular view in the ROI Controls lists the children ROIs, to the specified 
, of the currently . The currently is shown at the top of the table; users can navigate up and down the tree through the table controls. ROI Display Figure displays the most recently acquired image data at the specified ROI ID (and associated Position ID), while graphically depicting the same children ROIs listed in the tabular view. The ROI Display Figure also has a Top-Level ROI Selector View which can be used to quickly select among the top-level ROIs currently stored by ScanImage.
ROI File
: Displays name of the ROI file most recently loaded (if any)
: Saves current ROIs to specified ROI file (defaults most-recently loaded ROI file, if any)
: Prompts user to select file from which to load ROIs
See ROI Files for more information.
Position Tolerances & Calibration
: Specifies, in microns, the positional range within which a motor position will be considered to match a stored position value in the Position Controls table.
When motor position is considered a match, any added ROIs are stored in same tree hierarchy with other ROIs stored for that position.
: Specifies, in optical degrees, the angular scan range corresponding to one micron of lateral stage motion. This value is used as default value for certain macro operations, e.g. the and operations described below.
It is presently assumed that factor is equivalent in X & Y dimensions.
ROI Table
: A 'breadcrumb' string (e.g. 'ROOT ==> 2' as depicted) indicating the hierarchy of ROIs up to the rightmost identifier (e.g. 2 as depicted), which is the currently shown ROI whose children appear in the table below and whose most-recently acquired image is shown in the ROI Display Figure.
(Up Arrow): Updates to the parent ROI of the current – i.e. moves up the hierarchy. To move down the hierarchy, use as described below.
: Specifies number of generations of child ROIs of the currently to display, both in the table below and in the ROI Display Figure. Value of Inf indicates that all descendents of the are displayed, i.e. the ROI's children, children's children, etc.
: Update to the selected row (ROI) in the table
: Update ROI Scan Parameters and, if applicable, motor position to those of the selected row (ROI) in the table.
: If selected, automatically with every operation. The button is disabled.
: If selected, after going to a selected ROI (via , or with ), automatically take a Snapshot acquisition at the new ROI Scan Parameters and motor position (if applicable).
: Deletes currently selected row (ROI) in the table.
: Deletes all entries in the table, and their children. In other words, delete all descendents of the .
: Clears all ROIs that have been added and cached, for all motor positions.
Macros
These buttons launch macro operations to automate certain tasks related to the creation or use of ROIs.
: Macro that auto-creates positions and ROIs in a two-dimensional tiled array. Iterating through acquisitions at each of the created ROI/Positions, e.g. using Cycle Mode, allows the creation of a 'mosaic' image.
: Macro that creates a grid of evenly-spaced ROIs, with specified spacing, rotation, offset. The ROIs are added relative to an (also-added) top-level ROI with special Position 0 (non-position). The ROIs are shown in the ROI table and ROI Display Figure regardless of the last-read motor position value.
: Copies list of all ROIs shown in ROI table to the Cycle Controls, e.g. to allow automated or manual sequence of acquisitions at each of the ROIs.
: Show the ROI Display Figure (discussed below)
: Show the Position Controls.
: Saves current ROIs to specified ROI file (defaults most-recently loaded ROI file, if any)
: Prompts user to select file from which to load ROIs
: Selects whether to show ID labels in the ROI Display Figure
: ROI Display Figure displays the most-recently acquired image at the . If this option is selected, the maximum projection image will be computed and stored for stack acquisitions acquired at identified ROIs (i.e. matching RSPs and motor position of one of the cached ROIs) and displayed when that ROI becomes the .
: If selected, the ROI Scan Parameters are updated to match the added ROI when one of the graphical ROI Addition Tools is used on the Main Controls panel.
: If selected, a Snapshot acquisition is taken at the newly added ROI when one of the graphical ROI Addition Tools is used on the Main Controls.
: If selected, automatically with every operation. The button is disabled.
: If selected, after going to a selected ROI (via , or with ), automatically take a Snapshot acquisition at the new ROI Scan Parameters and motor position (if applicable).
: When is selected to goto a selected ROI (or is pressed with enabled) at a different motor position than the current coordinates, ScanImage will by default warn the user that a (potentially long) motor move will occur by going to that ROI. Deselecting this option will prevent this warning message from appearing.
and are linked to the and checkboxes on the Main Controls, respectively.
and are linked to the and checkboxes just below the ROI table.
