Hole Targeting Set-up for MSI-T » History » Revision 2
Revision 1 (Anchi Cheng, 12/01/2010 10:46 PM) → Revision 2/7 (Anchi Cheng, 12/01/2010 10:56 PM)
h1. Hole Targeting Set-up for MSI-T h2. h3. 1. Leginon/Hole Targeting/Original> Use this setting to load a test image if needed. * Select the Image Display Selection before opening the Image Display Settings window. * Browse the rawdata directory of the current session for an example image for testing. * Load the selected file and exit Image Display Settings window. * *If no file is selected while loading, an example square image will be loaded.* !square.jpg! h2. h3. 2. Leginon/Hole Targeting/Template> Targeting/Edge> A good template gives a sharp correlation at combination of parameters show the center edges of the holes. * Measure the hole diameter holes well with the ruler tool of the image viewer on any loaded original image of the hole to be tested. minimal thresholded "edge" from random features. * Select the Template Edge Display Selection before opening the Template Edge Display Settings window. * Enter the path Choose an edge detection Threshold and filename of the hole template file if it press "Test". "Test" should be done every time a parameter is not set previously. The template is normally an average of several images of changed to check its effect. * Adding a proper low pass filter can sometimes reduce the hole fragmented appearance of the same size and manufacturing method. edge image. * The [[Creating Template|previous section]] shows how Increase the template come with Leginon is created. Threshold if too many edges are shown in the edge image. * This default Use the ruler tool to measure the average inner and outer hole diameters for preparation on template has correlation. h3. 3. Leginon/Hole Targeting/Template> A good template gives a diameter sharp correlation at the center of 168 pixels. the holes. * Enter Select the hole diameter of Template Display Selection before opening the template under "Original Template Diameter" in pixel. Display Settings window. * Enter Click Add (Rings) and enter the inner and outer hole diameter diameters that were measured in the previous section. (Only one set of the hole diameters should be in the test image under "Final Template Diameter" in pixel. The ratio of the two diameters causes list. If a scaling set already exists, click Edit instead of entering the template. *Hint*: A larger final template diameter than the actual measure hole often give a sharper cross correlation peak. diameters.) * Choose a correlation method. "phase" "cross" correlation is the typical. * Set the typical for high contrast images. "phase" correlation works better with weak hole edges (i.e., thick ice) but should be used with a low pass filter. For example, increasing the filter = 2 or higher pixel size can reduce eliminating scattered sharp peaks found in phase correlation image. peaks. * "Test" these parameters and adjust. We found that adjust, normally, the best result often need the final template diameter to be set somewhat larger than diameters for sharpest correlation peaks at the actual hole in center of the image. !template.jpg! holes and exit the setting window. h3. 3. 4. Leginon/Hole Targeting/Threshold> A good correlation threshold leaves only small blobs of the correlation peaks from the holes. Since the peaks from holes with ice are usually weaker but more important to catch, it is o.k. to leave some but not too many noise peaks. This parameter also tends to change during an experiment. The value is in the unit of number of standard deviation above the mean. * While the template correlation image is displayed, find out the value of the correlation peaks using the information tool (with 42 shown on the button) * Select the Threshold Display Selection before opening the Threshold Display Settings window. * Enter the absolute or relative threshold Threshold value determined in the previous section and press Test. !threshold.jpg! h3. 5. Leginon/Hole Targeting/Blobs> If the threshold level from the last step is too low, there will be a lot of big blobs, making the process slow. The parameters set in this node reasonably limit the total number of blobs. * Select the Blob Display Section before opening the Blob Display Settings window. * "Border" should be set to at least the radius of the holes in order to reduce the border effects. * "Maximum number of blobs" is typically 300 (although it is sometimes larger if you expect more holes). * "Maximum size of blobs" should be adjusted until mostly hole centers, not junk spots, are shown. * "Test" and adjust the parameters in the last three steps (2-4) to acheive the best results. * To help define the lattice, measure the distance between hole centers with the ruler tool. h3. 6. Leginon/Hole Targeting/Lattice> The lattice of the holes is not perfect; therefore, a decent tolerance is necessary for a good fit to this imperfect lattice. If only a few blobs were centered in the last step, then this step is not likely to work. * Select the Lattice Display Section before opening the Lattice Display Settings window. * Enter the Spacing from the measurement in the last step. * Typical Tolerance = 0.1 (i.e., 10% error in the spacing is accepted) * Hole Stats Radius = ~ 3/4 of the hole radius. * Zero thickness = the intensity measurement from an empty hole at the same preset (the sq preset). * "Test" and examine the "mean thickness" and "standard deviation of thickness" in each hole on the lattice. h3. 7. Leginon/Hole Targeting/acquisition> The settings here depend on the required ice thickness and on the "Zero thickness" setting in the last step. At a minimum, these settings can be used to rule out holes that are empty and that have massive ice contaminant. * Select the Original and acquisition Display Sections before opening the acquisition Display Settings window. * Min. mean = ~ 0.05 measured by ln(I0/I) * Max. mean = ~ 0.3 * Max. stdev = ~ 0.2 * Focus hole selection = Good hole ( or "Any Hole" if hole targets are not plentyful. With "Any Hole" option,and a bad hole may be targeted that is hard to focus such as very thick ice. Alternatively, "Off" to skip the Z height correction step at each square ) * Use target template = no h3. 8. Leginon/Hole Targeting/focus> The only relevant focus setting ("Focus hole selection") in Hole Targeting is in relation to Z Height correction. The Leginon/Hole Targeting/focus Display Settings window = Leginon/Hole Targeting/acquisition Display Settings window. This means that the focus settings were set in the previous section and do not need to be revisited here. To see the focus targets, enable the Original and focus (and optionally the acquisition) display selections in the image control panel. h3. 9. Leginon/Hole Targeting/Settings> Activate automatic hole finding for future images received. Skip automatic hole finding = no