Launching scans/VP from 2D visualization

  • Wolfgang Theis

    Wolfgang Theis - 2010-01-12

    As I understand (not having an scanning probe running under GXSM, yet) all
    measurements are initiated through the HwI multi tab window or plugins. In
    many cases a point-and-click approach would be more natural, e.g. having
    scanned an SEM image and wanting to record a local Auger spectrum, or zooming
    into a region of interest. Is there a way to register a popup menu item which
    will take the x,y coordinates of the mouse click on a 2D visualization window
    and pass these on to a dialog to initiate a point spectrum? Similarly, can a
    rectangle on the 2D display be used to initiate a zoomed scan in a new window,
    or a mouse-click to center the scan area on a new position?

    For the MFM/SEM instrument (see post in "DSP new features requests
    (MK2-A810)") I would want to move a feature identified by SEM underneath the
    MFM tip using the coarse motion. In most geometries the MFM tip obstructs the
    view of the sample so that the sample has to be moved by a well defined
    distance and direction. This would require tracking the motion of the sample
    by comparing successive SEM images. Am I correct that this could be done with
    a dedicated plugin?

  • Thorsten Wagner

    Thorsten Wagner - 2010-01-12

    You can do that "point & click" by using image objects. So select the tool
    "object->point" by right clicking on the displayed image. Then you can add
    points within the image by left clicking. You can also move the points (and
    other) objects around. By using the middle mouse button you can set the scan
    offset to the coordinates of the last activated point. If you have checked
    "center scan" (the alternative is middle of the top) which is the default
    setting and should be found also within the HWI on the tab of the settings (or
    by a python script) your tip should move to that position as soon as you
    confirm the offsets. Then you can apply any type of (point) spectroscopy by
    the HWI. For zooming in on an rectangle use the crop function. So both in
    implemented :-)

    About your combination of the two instruments: If needed you can certainly
    have two SR attached to GXSM. Just in case you need further analog signals to
    control both instruments. The advantage is that you will have also the doubled
    memory, but of course inter board communication is more difficult. Anyway, I
    guess most of the correlation the two microscopes will be done by GXSM and not
    on DSP level. That will also help to keep the DSP code efficient and small.

    The amount of data for the motion tracking might be quite high - especially if
    you want to do that online with video rate. Maybe it is more suitable to
    calibrate the SEM image by moving the tip a certain length in all four
    directions and just compare the initial and the final position. You may get
    something like relative coordinates on the sample by just pointing on the tip
    position in the SEM image. Anyway, it would be thrilling to see GXSM operating
    at video rate with high resolution data.

    The plugins can access the channels of the Channel selector. It is no problem
    to subtract two images or so. Anyway for real time processing this might not
    be the best way to do it. You will need something like an image stack to be
    handled. I would do the real time view in a separate/special HWI just
    processing the data stream (without saving or further processing).

    Anyway, I thing what you want. We have a Jeol SAES here. You just point on a
    spot of the sample to acquire a spectrum there. Here is just an idea to get
    the correlation between MFM tip and SEM: Can you measure the current on the
    tip? By measuring the current as a function of time (or e-beam position) you
    can certainly figure out, how to move the tip by the coarse motion to get to a
    certain position in the SEM image.

    Thorsten :-)

  • Wolfgang Theis

    Wolfgang Theis - 2010-01-12

    Thanks for getting me up to speed on already implemented point & click
    capabilities, which are exactly those I was looking for.

    I see the advantages of using two SR boards. However, for financial reasons I
    would want to keep to one only. I suppose there is a question whether
    extending the functionality of GXSM systems with a single SR is worthwhile if
    the same can be achieved by buying a second SR. But I think there is also an
    interest to be able to provide a highly versatile and powerful GXSM system in
    its base configuration with a single SR.

    For the motion tracking I was just thinking of a loop of moving a nominal
    distance, taking an image, calculating distance moved. There is no need for
    speed here, i.e. it could be 20s scans and 50 micrometer or even larger moves.
    I haven't decided yet, but the tip could be 2-5mm to the side of the MFM tip.
    You are right, the alternative would be to move the MFM tip into the beam
    position, which would simplify finding the spot but add another coarse motion.
    I'm trying to keep both options open.

    On the GXSM side everything I was looking for seems to be available for


  • Wolfgang Theis

    Wolfgang Theis - 2010-01-12

    Meant to write: the MFM tip could be 2-5 mm to the side of the center position
    of the SEM beam.


  • Percy Zahl

    Percy Zahl - 2010-04-06

    One more note: About Zoom to selected area:

    Put a rectangle object to select the new area, then go to "Edit->Cpy Zoom In".
    This will generate a new scan with the old data just blown up to conserve the
    original scan area in pixels. Activate this new scan window -- this will show
    all proper new coordinates, offset/size, then just hit "Scan Start". At this
    point the current (new) coordinates/sizes will be used for the (or all if
    multiple channels) new scan(s) and you can close (kill) this temporary zoomed


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