- QuB tutorials - World3D

Transcription

1 - QuB tutorials - World3D April 2015 The MLab 1

2 World3D: Content Content: Start QuB Load Project Run Scriptlets to build World3D objects Navigate the World3D Load a World3D Setting up the camera LiveView Reposition LiveView and Pipettes Control the positioning motors Acquire images Memory issues 2

3 World3D: Start QuB When you first run QuB, it may look like this: Main Menu Current Interface Data Viewport Histogram Viewport Available Interfaces Model Viewport Report Viewport 3

4 World3D: Load a Project Load a Project: - Download the World3D Project example from: unzip the project - This Project loads a customized interface and several scriptlet libraries, prepared for this tutorial - Open project from the Main Menu: Main Menu > Project > Open Project Project interfaces are automatically saved. If you would like to revert to the original interfaces, choose Revert to saved Workspaces: Main Menu > Project > Revert to saved Workspace 4

5 World3D: Load a Project After loading the Project, QuB will look like this: Scriptlets: 3D Scene Viewer World3D Object Tree All objects are listed here World3D Interface is selected Predefined World3D Objects Scriplets Viewport World3D Viewport 5

6 World3D: Create 3D objects using KPL You can create additional objects in the World3D, using the KPL scripting language: - Run the Make 3D World scriptlet in the Scriptlet Viewport (Mouse-LClick) - The scriptlet will create a rig equipped for electrophysiology and imaging Run this Scriptlet (Mouse-LClick) 6

7 World3D: Create 3D objects using KPL After running the scriptlet, you will see new World3D objects : New 3D objects created with the KPL scripting language 7

8 World3D: Navigate the World3D scene viewer You can navigate in the World3D scene viewer with the mouse and keyboard: Mouse: Left button: Right button: Scroll wheel: Rotate World around the center of the selected object. To select an object, Double-Click on it Translate the position of the observer relative to the world Move the observer closer or farther from the world (+Ctrl for finer movement) Keyboard: Up/Down: Left/Right: Shift + U/D: Ctrl + U/D/L/R: Same as Mouse scroll wheel Translate observer left/right Translate observer up/down Rotate world around observer *If you want to reset the position and rotation of the World, right click and choose Viewer camera and then Reset. 8

9 World3D: Navigate the World3D scene viewer After playing with the mouse, your World3D might look like this: 9

10 World3D: Scriptlets A scriptlet contains KPL code that can be run by pressing a button - Scriptlets are organized in Scriptlet Libraries Scriptlet Libraries 10

11 World3D: Scriptlets For example, you can turn on the laser by running the 2P Laser Beam On/Off scriplet, located in the Microscopy scriplet library. - After doing this, you should see the laser beam 11

12 World3D: Scriptlets You can edit or inspect the code in a scriptlet: - Open the scriptlet editor by Right Clicking on a Scriptlet - Select Edit Scriptlet 12

13 World3D: Save to / Load from a file The content and settings of the World3D can be saved/loaded as a file. - Currently, only the objects under the Virtual category (Images, Contours, Data, etc.), as shown in the Object Tree, can be saved in a World3D file - World operations are accessible through the Main menu or through buttons: World3D buttons (New/Open/Save) 13

14 World3D: Load a World3D example Load a World3D: - Download the BrainMapExample.zip from: unzip the file - This World3D is a collection of images and data - Open World3D from the Main Menu (or using the buttons): Main Menu > World3D > Open World3D 14

15 World3D: Load a World3D example After loading the World3D example, you will see this: 15

16 World3D: Load a World3D example Let s hide the Physical Objects so we can better see the images: - click the buttons that show/hide the Physical and the LiveView: Show/hide the Physical world Show/hide the LiveView 16

17 World3D: Load a World3D example After hiding Physical and LiveView, you will see this: World3D content, in this case just images and data 17

18 World3D: Load a World3D example Navigate with the mouse to better see one of the 2P stacks: 18

19 World3D: Load a World3D example To select objects in the World3D: - Double-Click on an object in the 3D scene viewer selects the object - A selected object becomes the center of rotation for navigation - The position and rotation of the selected object is shown here (Double-Click on selected object name to switch between position and rotation): Selected object Position Rotation 19

20 World3D: Load a World3D example To select objects in the World3D: - Alternatively, you could also select an object from the Object Tree - The object does NOT become the center of rotation Selected object 20

21 World3D: Set up the camera Set up the camera: - Select the Camera interface Camera display Camera settings (click on caption bars to expand / collapse panels) Select Camera interface 21

22 World3D: Set up the camera Set up the camera: - Rearrange the interface - Close the Report Viewport and resize the Camera Viewport Click and drag to resize viewport 22

23 World3D: Set up the camera Set up the camera: - Open the simulated camera - Right-click on the camera display and select Open sim camera Click to start continuous camera acquisition Check this option to have the image taken by the camera displayed in the World3D, in the LiveView Lens area (Check Lens in the Viewer panel and change the zoom factor to see the lens effect) Sensor cropping area (check Cropping in the Acquisition panel to activate it. Must stop and restart image acquisition) 23

24 World3D: LiveView Set up the LiveView: - Select the World3D interface - Show Physical and LiveView Show/hide the Physical world Show/hide the LiveView 24

25 World3D: LiveView Set up LiveView: - You should now see something like this: (if you don t see it, click again on Show/Hide Physical and LiveView buttons) LiveView LiveView content is refreshed as long as Camera is running 25

26 World3D: LiveView Set up LiveView: - Now load again the BrainMap example (if you had it closed) - Turn off (hide) the Physical objects - Now you see the LiveView in the context of the brain map: The physical size of the LiveView image 26

27 World3D: LiveView Reposition the LiveView in the World3D space: - Select the LiveView, using one of these procedures: - select LiveView in the Object Tree, or - double-click on LiveView in the Scene Viewer, or - click the Viewport button (LiveView is contained in Viewport). Selecting the Viewport selects LiveView, and vice versa 27

28 World3D: LiveView Reposition the LiveView in the World3D space: - Once LiveView / Viewport is selected, it can be repositioned in the WorldD space using one of these procedures: - click the positioning buttons, or - enter new position coordinates and set them with the Set button Viewport / LiveView position coordinates (or Pipettes) Set position coordinates for Viewport / LiveView (or Pipettes) Positioning buttons to interactively move the Viewport / LiveView (or the Pipettes) 28

29 World3D: LiveView Reposition the LiveView in the World3D space: - Try to move the LiveView Up and to the Right, using the interactive buttons - Notice that x and y movement keeps the LiveView immobile but moves the Virtual objects (Images, Data, etc) 29

30 World3D: Pipettes Reposition the Pipettes the World3D space: - The Pipettes can be repositioned using the same procedures as for LiveView - Show the Physical world, zoom out a bit using the mouse scroll bar, then click on the right Pipette, and you will see something like this: Pipette1 selected and ready to be repositioned Pipette2 Pipette1 30

31 World3D: Motors QuB can control the positioning motors associated with the objective, the pipettes, etc. - Currently, QuB works with motorized positioners via ScanImage ( ScanImage is also used for image acquisition with a two-photon microscope. The ScanImage version we tested was slightly modified and can control only the translation stage and the objective. - We are working on implementing direct motor control within QuB for Scientifica positioners. Extension to other brands will be possible, if the manufacturers provide a communication interface for software control. - Please check for updates on motor control. - For now, test QuB without activating the motors. In this case, the liveview will not follow the objective and vice versa. 31

32 World3D: Image acquisition Set up Image acquisition: - First, turn Physical off - In the Acquisition panel, select Hi magnification and enter new values for image size (w = 332.8, h = 332.8) - Make LiveView the center of rotation by double-clicking on it - Set LiveView coordinates as (0, 0, 300) and press Set - Navigate in the World3D to get closer to the LiveView 32

33 World3D: Image acquisition Set up Image acquisition: - You will see something like this: 33

34 World3D: Image acquisition You are now ready to acquire images with the simulated camera, using multiple paradigms: - Acquire a single image - Acquire a stack of images, scanning any combination of the x, y, and z axes - Acquire a stack of images as defined by a volumetric contour - Acquire a time series of images, at a single position 34

35 World3D: Image acquisition Let s set up acquisition of a z-stack: - Set Acquisition parameters exactly as shown in the screenshot - 10 images will be acquired across the z-axis, with 10 micron step The number of images to be acquired on each axis Increment for repositioning the LiveView on each axis during image acquisition. Acquire a single image Acquire a time series Acquire a stack of images, as defined by Image count and Pos increment Acquire a stack of images, as defined by a volumetric contour 35

36 World3D: Image acquisition Press the Stack button and you will see something like this: Newly acquired stack 36

37 World3D: Image processing Let s change how the stack is displayed: - First, make sure the stack is selected: double-click on it - In the Images and LUT panels, set parameters as shown (Brightness and Contrast are 0 and 1, respectively) 37

38 World3D: Image processing Let s change the color to Green, change the LUT values, and make the stack transparent: 38

39 World3D: Memory issues After this image stack has been created, you might notice that your World3D scene viewer is no longer very responsive to navigation - The explanation is that you have now a lot of pixels to display, and the video card slows down - If you acquire any more images, you will probably run out of CPU or video memory, and QuB might even crash - To prevent this, you can unload some of the existing images, by right-click and selecting Close - Another possibility is to downsample an image, by right-clicking and selecting Downsample Nx, where N is a factor between 2 and 32 When you close QuB, make sure the Camera is stopped 39