Specimen Navigation
Using the Navigation functions
The specimen can be navigated through the X, Y and Z axis (where available) using the on-screen joystick functions. An overview of the navigation settings is shown in Navigation Settings.
Using the Joystick to navigate through X and Y axes
The joystick can be used to move the stage through the X and Y axes. A small sub window appears in the main image viewing window showing the stage position.
Above - Using the on-screen joystick for navigation. Note the sub-window showing the current stage position.
The position of the Stage Position sub-window can be adjusted to appear in a different corner of the image viewer panel. To do this, click the box that corresponds to the corner of the image viewer panel you want the sub-window to appear at (the default is top-right).
Above - Setting the position of the sub-window, shown from left to right: top left, top right (default), bottom left, bottom right.
The speed of the joystick can be set between the default coarse (faster) movement, fine (smaller) movement or Superfine (even smaller again). These step sizes can be changed in https://oiandor.atlassian.net/wiki/spaces/fusionum/pages/7570006/Navigation+Settings Preferences) Click to open the menu and select.
Above - Fine movement mode activated for joystick navigation for both XY and Z.
You can also use the nudge function keys around the joystick to move the stage in a large, or small increments:
Above - Top: the large nudge key and Bottom: the small nudge key. Values for these can also be set in navigation preferences.
NOTE - If this (software) stage joystick is not functioning as expected, please refer to the F.A.Q.
Navigating through the Z-axis
It is also possible to manually navigate through the Z- axis (where available) using the Z-axis joystick. Depending on the system being used, this could be the microscope (also known as Ref Z) or the Piezo. The appearance of the joystick will change depending on whether a microscope or piezo is available. If both are available, the microscope will be used.
Above - Using the Z axis joystick to move the microscope Z
The speed of the joystick can be set between the default coarse (faster) movement, fine (smaller) movement or Superfine (even smaller again). These step sizes can be changed in https://oiandor.atlassian.net/wiki/spaces/fusionum/pages/7570006/Navigation+Settings Preferences) Click to open the menu and select.
Above - Fine movement mode activated for joystick navigation for both XY and Z.
You can also use the nudge function keys above and below the Z-axis joystick to move the stage in a large, or small increments:
Above - Top: the small nudge key and Bottom: the large nudge key. Values for these can be set in Navigation Preferences.
Setting bounds
Above - the top left bound has been set.
Set bounds for the top left and bottom right corners. This can be used to ensure you don't navigate away from the region of interest within a sample completely. A sub-window will appear to highlight the current position of the stage within the set bounds.
The Lock and Unlock buttons let you lock or free the set bounds as required, while Clear removes the set bounds completely.
Specimen Overview
Quick WxH Montage: Clicking the button will take a montage of the sample of the specified width and height around the current stage position. Moving the stage to a new position and clicking the button will add the montage from the new position to the existing specimen overview so that the image of the specimen can be built up incrementally. If the button is clicked more than once without moving the stage between clicks then the montage at that stage position will be expanded by one tile in each direction. Note that changing to a different channel and clicking the button will result in the entire specimen image being cleared and restarted with the new channel. When using Quick Montage, only the montage tiles that are not already present in the specimen overview will be imaged.
This button switches to the file gallery window where previously built specimen overview images can be loaded.
Click to navigate: When enabled, this option allows you to click any point on your image and the stage will navigate to this position. This is useful when defining a Multi-Position protocol. A field position indicator will appear on the image when this mode is enabled showing the area of the sample that is currently in view by the camera. The field position indicator tracks the position of the stage and the magnification of the system to provide an up to date indication of the current view. When Live acquisition is initiated the image shown will correspond the the area shown by the field position indicator.
