Position Save Module

Run by the optional module, PositionSave_coMD.vi, the position save module allows the user to save and recall XYZ motor positions. The module uses both the current XYZ motor positions (absolute positions) as well relative XYZ positions based on a pre-set origin, allowing the positions to be used even if the XYZ motors coordinates are re-set or if the sample shifts relative to the motors between experiments.

Along with a text file detailing the XYZ position, a snapshot of the current Field of View is saved in a time-stamped folder for later reference and re-positioning.

Position Overlay GUI
Position Save Module (PSM) User Interface
AImage Display Link to SciScanCurrent Image DisplayLatest image acquired by the SciScan software and is the same as what is displayed on the main UI
BSaved Image DisplayImage saved during a 'position save'. The user can browse through all saved position images
CStage Control, Links to SciScanXYZ Stage controlThis is a replica of the stage control provided in the main UI to move the stage in XYZ to find points of interest.
DLink to SciScanChannel Selector Selection of the acquisition channel, which is displayed as ‘current Image’ (This corresponds to the channel tab selected in the main UI).
EFocus ButtonFocus at current position and displays image
FOverlay FunctionOverlay Button Enable/Disable the overlay function
GOverlay ControlsSettings to auto scale or manually scale the levels of red and green in the overlaid image.
HGridGrid OverlayOverlays an adjustable size grid on both the live image and reference image to aid in position alignment
IFile OperationsCopy ButtonMake a copy of the current data file at a user specified destination
JFile PathDisplays current data file path
KX-Y Plot of saved positionsThis displays current stage position, origin, saved positions and position selected in the table relative to one another.

Position Save Functionality
Table DisplayDisplays all the saved positions along with their time stamp and provides an editable notes field. Selected fields are highlighted green
MPosition browser clusterBrowse through the different table entries (saved positions). Alternately the Up/Page Up, Down/Page Down, Home and End keys on the keyboard may be used.
NCore Functionality Set POI - Sets a position of interest

Go To - Go to the position currently selected in the table

Delete - Delete the position currently selected in the table

New List - Creates a new position file and related folder hierarchy in the hard disk

Load List - Loads a position file from hard disk

Set New Origin - Changes the origin to the current stage position

Notes on Use

Launch the position save module using the button provided in the stage control section of the UI. The interface can be hid again by pressing the hide button found near the motor controls, all values are saved when the UI is hidden.

Before the module can be used, either a new list must be set up or an old list must be loaded.

  • Press the New List or Load List button in the bottom right to launch the explorer window and either navigate to an existing list or choose a file path where you would like your position data to be saved.

Setting up a new position list

The first thing that needs to be done when setting up a new list of positions is setting an origin, none of the other functions are available until an origin has been set. The origin should be a recognisable structure that can easily be found at the beginning of an experiment. e.g. a unique blood vessel pattern near the surface of the brain.

In order for the origin to be set, or any other position to be added, there must be a live image displayed in the current image window, press Focus to bring up a live image.

Setting the origin will add the first line into the position table complete with absolute motor coordinates and relative coordinates (will always be 0,0,0 for the origin). The notes section on the far right hand side of the table is editable and can be used to make notes about the position – these notes are also saved along side the positions for later reference. On top of populating the table with the position information the module also takes a snapshot of the current field of view and saves it in the same folder.

Once the origin is set the user is free to move around the sample and add additional points of interest using the Set POI button. Each addition will add a line to the table and add a position marker on the XY plot, showing where each position is located relative to one another. Every time the table is edited through the addition or removal of a point of interest, the file that stores the list is automatically updated, make sure the file is not open in another program to ensure it can be written to.

Positions can be recalled by either selecting the appropriate line of the table and pressing the Go To button, or by pressing the Enter key on the keyboard. Positions can be navigated between using the arrows provided, the arrows on the keyboard or the Home and End keys on the keyboard.

Returning to an old position list

The Position Save Module is designed with chronic imaging applications in mind and allows users to return to the same field of view days or weeks later, with high repeatability.

Press the Load List button in the bottom right of the UI and navigate to and select the position list that you would like to load.

Once loaded the table should auto populate with the positions that were previously saved to the list.

Repositioning a sample exactly as it was in a previous experiment is very difficult and it is likely that the saved motor coordinates will no longer relate to the same positions within the sample, this is where the position save module comes into its own. To overcome this issue and allow the same fields of view to be imaged again the user needs to find the previous origin and from there, the relative positions that are saved alongside the absolute positions can be used to return to the old memory positions.

When a memory position is selected it’s snapshot is displayed in the Saved Image pane. The Overlay switch located between the two display windows creates a Red/Blue overlay image between the saved image and the current FOV. This feature can be used to correct for any inconsistencies in positioning between the two experiments.

Navigate to the origin using the position save feature. If the sample has not been mounted exactly as it was previously, the saved snapshot and the current image should not match which can be made obvious by using the overlay feature, as shown below:

Image overlay mismatch
Image overlay mismatch. N.B Image shows previous red/green overlay colour scheme.

By moving the stage slightly you should be able to bring the red and the blue image into alignment, creating a purple image and confirming that you are now back in the exact position where the origin was set previously. Press Set Origin to shift the position values stored in the table to those that correspond with the same origin’s current location. Whenever the origin is shifted, all of the XYZ values for the other saved positions are shifted by the same amount. With the correction made, the user should be able to freely navigate to all of the previous memory positions, providing there hasn’t been a relative shift in position between them and the origin.

Image overlay match
Image overlay match. N.B Image shows previous red/green overlay colour scheme with yellow indicating alignment. SciScan 1.1.5 will show purple where red/blue images have been correctly overlaid.

Grid Overlay

In addition to the Red/Blue overlay, a grid can be can overlaid over the images to aid in aligning the current image with the saved reference image. To overlay the grid onto the images use the grid slider to adjust the number of cells shown on the image. Cell numbers can be adjusted between 1x 1 cell (no grid), up to a grid of 20 x 20 cells. This can aid alignment of the current field of view, especially in applications where the overlay feature is not enough. To learn more about the grid overlay feature please see the relevant galvo or resonant pages.


Only for v1.4: red and blue overlay options available

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