positioning

Tiling with Knobby

Knobby scheduler allows the user to move the microscope by specifying a list of relative changes in position at given frame numbers.  One quick way to fill up the table is provided by a set of text fields in the knobby panel.  This allows one to perform (x,y,z) tiling with a given range and step size.

tiling

The first row of entries correspond to the range (in um) to be covered in the x, y and z axes respectively.  The second row specifies the step size in each case.  The last entry at the bottom tells Knobby how many frames to sample at each location.

In the example above, Knobby will perform a z-stack with 40um range and 20 um steps (that is, a total of 3 locations), on an (x,y) grid of 3×3 with 200um horizontal and vertical range and steps of 100um.

As you input the desired values the table will update automatically.

Once ready, click the “Arm” checkbox (and the “Return” checkbox if you want knobby to go back to its initial position at the end) and start your acquisition.

Here is the resulting scan for the example above:

Click-and-Center with Knobby Mouse Control

If you have been making use of Knobby’s spatial calibration button, you can now move on to interacting with Knobby remotely.

The new Knobby scheduler panel looks a bit expanded.  The speed (coarse/fine/super-fine), the mode (normal/rotate), and zero (XYZ/XYZA) buttons should be self explanatory. They do exactly the same as if you were to be using them on Knobby.  The action you select on the panel will be reflected on Knobby’s screen as well.

knobbymouse

The range, steps and frames entries provide a quick way to edit the scheduler’s table if you intend to do a simple z-stack.  Range is the extent of the distance in z you want to span, steps is the the size of the step (in um), and frames is the number of frames you want to scan at each position.

Finally, there is new checkbox labeled “Mouse control”. When this is active and you are scanning you can easily move around the sample by clicking the cell you want to bring to the center of the screen, as shown by the video example above.  Once you click on a cell, Knobby does the rest. We call this feature click-and-center. This works at all magnifications (even if you change it on the fly). At the same time, scrolling the mouse wheel allows you to focus up and down.  The speed of the movement will be controlled by the selected speed. You may want to start at the slowest speed (Super-fine).

Installing knobby tablet

Before you start you will need an android tablet and a wireless router in the Lab.

I have a Samsung Galaxy Tab E and an Airport Express, but other tablets and routers should work as well.

To install knobby tablet follow the following steps:

  1. Download knobby tablet from the Google Play store.
  2. Download and install the latest version of Scanbox (as always keep a copy of previous version).
  3. Download and install PyOSC.  To install, open a terminal, go to the directory where you uncompressed PyOSC, and type “python setup.py install”.
  4. Copy over the settings in the scanbox_config.m file.
  5. Connect the computer running Scanbox to your local wireless router
  6. Open a terminal window and check the IP assigned to the computer by typing ifconfig.
  7. Set the tri_knob configuration variable in scanbox_config.m to a string that contains the IP address, for example, ‘164.34.123.31’.
  8. Start Scanbox.  You should also get a command window with the knobby tablet console.  We will check if commands from the tablet are received there.
  9. Open knobby tablet on your Android.  You will likely get a message saying that the default IP is invalid.  Click Ok.
  10. Click on the IP number button.  A keyboard will show up.  Enter the IP number you found above.  However, make sure that every section has 3 digits (use zeros if necessary).  Thus, in the example above, one would type 164.034.123.031
  11. If the tablet cannot connect, you will see an “Invalid IP” message.  Otherwise, you should be ready to go.  The IP gets stored in the tablet, so launching knobby tablet later will retrieve it.
  12. Remove the objective from the microscope (just in case).
  13. Make sure the scope is roughly in the middle of its travel for all axes.
  14. Click the “Normal” button on the tablet.  Do you see a message printed on the knobby console?  If so, communication is working Ok.  If not, something is wrong.  Contact me.
  15. Stand close to the motor box so you can quickly power it off if something does not work as expected.
  16.  Now touch the button corresponding to the Z axis on the red region.  The z-axis will begin to move so long as you keep touching it.  The speed of movement will be faster the farther away you are from the center.  Slide your finger left and right, the speed will change and it should reverse if you move over to the blue side.
  17. Test the other axes.screenshot_20161112-150708
  18. Touch “Velocity” to switch to velocity mode.
  19. Warning: the microscope will move fast now…  Touch the red or blue areas of each button.  The microscope will move at a fast/fixed speed so long as you keep touching the area.  It will stop when you release.
  20. Store/Recall buttons work as before
  21. Go back and try the Fine and Super-Fine modes.
  22. Play with it for a while and install the objective back after you familiarize yourself with the tablet interface and everything seems to be working Ok.
  23. You can minimize the knobby console once testing is done (I will do this automatically in future versions).
  24. The green buttons on the side lock the button area (bottom) or knob area (top).  So if you are acquiring data and don’t want to have a situation where people touch the tablet by mistake and move the microscope you can use the buttons to lock them.  Touching them again will unlock.
  25. Make sure you open knobby on your tablet  after you start Scanbox.

If you run into problems don’t hesitate to write.

 

 

Better positioning with a wireless 3D mouse

The latest Scanbox release switches its positioning mechanism to rely on the 3dconnection wireless SpaceMouse.  A single controller provides a more intuitive, responsive and smoother control of microscope position.  It is more intuitive because the panning controls align with the axes of the microscope, and a twist motion of the knob allows you to rotate the objective.

3dmouse

With the 3D mouse it is no longer necessary to specify an axis before movement — you just move the joystick in the desired direction and the axes will be selected.  It also provides two buttons that allow switching between coarse/fine motion and normal/rotated modes. The interface is and faster through java-based listeners that take care of the motion without interfering with data acquisition and display.

imgres

Because the communication and control methods with the motor control box have changed substantially, the older ShuttleXpress wheel will no longer be supported in future releases.  So make sure you have your 3D mouse before upgrading to the most recent version of Scanbox.  It can be obtained here.