Capturing a Layer

This tutorial will show you how to capture a layer.

Creating a New Project

  1. Go to the File tab and click on New Project.


  2. Specify a name and location for the project. Leave the Template field as Default for now. For more information about templates, see the tutorial on Logging Additional Information.


    Click the Create button to create the project.

Connecting the Stage

  1. Go to the Capture tab and click the Stage button.


  2. Set Type to MSI-2 w/Rotation.

    Set Port to the com port that is connected to the stage. The stage must be powered up when Pix2Net is started, or else you will not see the stage’s com port in this list. If you are unsure about the correct com port, you can go to Control Panel -> Device Manager and look at the entries under Ports (COM & LPT). If you connect and disconnect the stage’s USB cable, then one of the com ports should appear and disappear.

    The Y-Axis should be inverted, so that the screen will pan down as the y coordinate increases, and the screen will pan up as the y coordinate decreases.

    The Home on Connect button should be checked if this is the first time you are connecting to the stage after the stage has been turned on.


    Click the Connect button to connect to the stage. It will do a homing process that takes a minute, and then the stage will be ready.

  3. Click the Manual Move button.


  4. In the Manual Move panel, enter coordinates into the Stage X and Stage Y fields. Press the green button to move the stage to those coordinates.


    The SEM image should move right if the x coordinate increases, and left if the x coordinate decreases. The SEM image should move down if the y coordinate increases, and up if the y coordinate decreases.

Connecting the Camera

  1. Start the Pix2Net Server on the SEM computer. For more information about the Pix2Net Server, see the tutorial on Capturing an Image.

  2. Click the Camera button.


  3. Set the Type to Microscope and click the Connect button.


  4. To capture a test image, click the capture button in the Manual Move panel.


Aligning the XY Stage to the Device

Before capturing the layer, you must use the Pix2Net rotation stage to rotate the device until the device is aligned with the Pix2Net XY stage. You can not use the SEM’s rotation stage to accomplish this, because the SEM’s rotation stage will rotate the Pix2Net stage and the device simultaneously. You can adjust the Pix2Net’s rotation stage manually in the Manual Move panel, but it is usually easier to use the Rotation Alignment feature.

  1. Click the Rotation Alignment button.


  2. Follow the instructions in the Rotation Alignment window, and then click the Next Step button to perform coarse alignment.


  3. Continue to follow the instructions in the next two steps to perform fine alignment.

Setting up a Run

  1. Click the Capture Config button.


  2. Click the Show options button to bring up the options.


  3. In general, these options rarely need to be changed, but it is good to be aware of these settings:

    Overlap determines how much the images should overlap with their neighbors.

    Stabilization Time determines how long Pix2Net should wait for the stage to stop moving before it captures an image. If this amount of time is too short, the stage may still be moving slightly as the image is captured.

    If you turn on Backup Images, and specify Backup Location, then a copy will be made of each captured image in the backup location.


    Click Cancel to close the options dialog.

  4. Click the New Area button. Enter a name for the new area. The Copy values from field allows you to initialize an area with the values from an existing area, but since this is the first area you are creating, it must be set to [None]. Click Create.


  5. Fill out the layer properties.


    The X, Y, Width, and Length properties define the location and size of this area.

    Pixel Width will be used to determine the number of images that must be shot to capture this area.

    The rest of the properties are optional.

  6. Fill out the focus settings.


    • Do not adjust focus - If you select this option, then Pix2Net will not adjust the focus during the run.

    • Dynamically adjust focus - If you select this option, then the focus will be automatically adjusted every time that Pix2Net moves the stage the specified distance along each row. For example, suppose that the specified distance is 5 um and every row is 12 um long. In that case, the stage will be adjusted 3 times during each row: Once at 0 um, again at 5 um, and one last time at 10 um.

    • Create a focus adjustment schedule - If you select this option, then you can create a focus adjustment schedule by specifying the desired focus amount at different locations on the device. The nice thing about specifying a focus adjustment schedule is that a scheduled focus adjustment is faster and more reliable than attempting to dynamically adjust the focus. You can manually add points to the table, but an easier way to fill out the table is to use the focus adjustment controls in the Manual Move panel. Go ahead and click Save to save this area, and then look for the focus controls on the Manual Move panel:


      Move the stage to the upper left corner of the device, make sure that the focus looks good, and then click the Add Focus point to add this point to the table. Move to the upper right corner of the device, use the Go to specified focus value button to adjust the focus, and then add another focus point. Repeat this procedure for the lower left and lower right corners of the device. Open the Capture Config window again. You should now have four sampled points in the sampled focus point table.

      Finally, if you are worried that the ideal focus will change over time, you can select In additional, dynamically adjust focus at the beginning of each row. In that case, when Pix2Net moves the stage to the beginning of a row, it will apply the scheduled focus adjustment first, and then it will dynamically adjust the focus.

  7. You can get an estimated capture time by setting the correct Tile width, Tile height, and Time per tile.


  8. Click the Save button to save the area you just created.

Starting a Run

Click the Start button to start the capture.


Pix2Net will start (or resume) the first enabled area in the list of areas to capture. Once Pix2Net finishes that area, it will disable it, and move to the next enabled area. If there are no more enabled areas, Pix2Net will stop capturing.