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Next: Autoindex and strategy calculation
Up: Web-Ice
Previous: Getting Started
Subsections
  • Selecting an Image File
    • Displaying the last image collected
    • Using the file browser for image selection

  • Displaying the diffraction resolution
  • Adjusting Image Display
    • Panning
    • Zooming
    • Adjusting Brightness
    • Changing Size

  • Image header
  • Analyzing the image


Image Viewer

The Image Viewer is used to view and analyze diffraction images located on the file server at SSRL. The image files are subject to the Unix security restrictions: The user must have a read permission to the image file in order to load and view the image.

The viewer comprises three frames. The left frames displays a JPEG of the selected diffraction image. The file path of the displayed image file is shown above the JPEG image. Next to the image there is a control panel for adjusting the image display parameters, such as zooming and panning.

Figure 2: Image Viewer.
Image image

The right frame displays either the selected image header or, when images analysis is requested, the analysis results.

The bottom frame is a file browser that allows the user to select an image file and explore directories. The starting search directory will be the one set in the Preferences tab.

Selecting an Image File

Image files must be in the MC file system and be readable by the user. There are three ways to select an image to be displayed:

  1. Type in an image name (full file path) in the text box below the image display box in the left frame. The file path typically begins with /data/username or /home/username, for example:
    /data/joeuser/images/remo_1_001.img.

  2. The second way to select an image is to use the file browser in the bottom frame as explained below.

  3. The third way is to click on the Prev or the Next buttons, located on the right side of the display image. These buttons only work if an image has already been loaded. The Prev button loads an image with the immediately lower index than the current image. For example, if the current image is remo_3_015.img, clicking the Prev button will load remo_3_014.img. Similarly, the Next button loads the image with the next higher index than the current image. In the previous example, clicking on the Next button instead, will load remo_3_016.img. If the current image is the first or last image in the dataset, clicking the Prev or Next button respectively yields no effect.


Displaying the last image collected

If the user has selected a beamline where an experiment is being carried out, the Last Image button will be active. By clicking this button the user can display the latest image written to the directory by the beamline control software.


Using the file browser for image selection

The first line in the file browser displays the current directory. Clicking on [Refresh] will reload the directory contents (this is useful, for example, if new images are being continuously written to the directory).

Clicking on [Up] will change the directory to the parent of the current one. The following lines are links to subdirectories or image files. File permissions, file/directory name, size in bytes, last modification date and time are displayed for each file. Clicking on a subdirectory name will list the contents of that subdirectory. Clicking the link for an image file will display the image.

Note that the user can only browse files and directories that have a read permission for their Unix login id.

Displaying the diffraction resolution

Moving the mouse over the diffraction image will display the resolution in the box below the image.

Figure 3: Displaying the resolution at the mouse position in the Image Viewer.
Image resolution-box


Adjusting Image Display

The user can zoom, pan, adjust brightness and set display size of the image by using the image control panel located to the right of the displayed image.

Panning

There are three ways to pan the image. One is by clicking on the image. The image will be moved so that the mouse click position will be come the center of the display.

The second way to pan the image is by using the thumbnail located at the top of the image control panel. When the zoom level is greater than 1 (the image is zoomed in), the thumbnail displays a red rectangle representing the area of the image being displayed. The more the image is zoomed in, the smaller the rectangle. The user can click anywhere in the thumbnail to move the rectangle.

The third way to pan the image is by clicking one of the pan buttons, which are located below the thumbnail and above the zoom buttons.

Zooming

The user can zoom the image in and out by using the zoom buttons or by entering a zoom level in the zoom text box. When the image is zoomed out to the maximum, the zoom is level is 1.0; it can not go lower than this. The higher the zoom level the more zoomed in the image. The left arrow button is for zooming out and the right is for zooming in.

Adjusting Brightness

Brightness of the image is controlled by the Brightness buttons and text box below the zoom buttons. The left arrow button makes the image darker and the right button makes it lighter. The brightness range is usually between 100 - 2000. The lower the number the darker the image. Brightness of 200-500 is typically good for most images.

Changing Size

By default the image size is 400 by 400 pixels. The user can change the image display size by selecting a different size from the drop down menu located under the brightness buttons.

Image header

The image header is retrieved via the image server. The header displays useful information about the image.





Table 1: Header fields for a Q4 image
Header Name Description Example
OVERLOAD_CUTOFF The maximum intensity 65535
  value for each pixel  
HEADER_BYTES Length of the header 512
DIM Image dimensions 2
BYTE_ORDER Machine byte order little_endian
  (little or big endian)  
TYPE Type of stored value for each pixel unsigned_short
SIZE1 Width of the image in pixel 2304
SIZE2 Height of the image in pixel 2304
PIXEL_SIZE Size of the pixel in cm 0.0816
BIN Detector binned mode none
DETECTOR_SN Detector serial number 403
TIME Exposure time 30.041451
DISTANCE Detector to sample distance 175.000000
PHI Phi 89.000000
OSC_START Starting Phi/Omega 89.000000
OSC_RANGE Oscillation range 1.500000
WAVELENGTH Wavelength in Angstrom 0.979413
BEAM_CENTER_X Beam center X in mm 94.000000
BEAM_CENTER_Y Beam center Y in mm 94.000000
PIXEL SIZE Size of the pixel in mm 0.0816
EXPOSURE TIME Exposure time in seconds 30.0415
TWO THETA Two-theta angle of the detector 0
  (not supported at SSRL)  
DETECTOR Detector name ADSC QUANTUM4


Analyzing the image

When the user clicks on Analyze Image, Web-Ice will run LABELIT (SPOTFINDER module) to analyze the image. The results of the analysis will be displayed under Spot Statistics in the right hand side frame of the Image Viewer page. Alternatively, the user can choose to perform image analysis automatically for each image selected by setting this option in the Preferences Tab. When the image has been analyzed, the user can use the Show spot overlay check box to toggle between displaying the highlighted spots, ice rings and resolution limits or the original image.

The output image displays the following features:

  • Good spots (potential Bragg spots): green border
  • Dubious spots (overloaded, weak, ice diffraction, etc.) : yellow border.
  • Spot maximum pixel: White dot (more than white dot in a spot indicates multiple maxima).
  • Initial estimate of the resolution limit: Green circle.
  • Ice rings: Orange circles.

The results displayed by Web-Ice include:

  • Number of good Bragg candidates

  • Average spot model eccentricity: The closer to 0, the more circular the spots are. Very high values (around 0.8 or higher) may indicate high mosaicity.

  • Number of ice rings.

  • Resolution estimate

  • Maximum cell edge estimated from the distance between candidate Bragg spots.

  • Saturation (percentage of the overloaded value) for the strongest peaks. If it exceeds 50%, there may be too many overloaded spots.

  • Number of spots with overloaded pixels

  • A score for the image calculated as follows:

    1. A score is assigned depending on the resolution (ranging from 14 for resolution higher than 1.5 Å to 1 for lower than 8 Å.
    2. The score is then adjusted by -5 to +4 points depending on the diffraction strength, spot shape and number of ice rings.
    3. finally the score is normalized reset so that the minimum score is 0 (for no diffraction).

Both the log and the overlaid image file generate by SPOTFINDER are saved in the directory
/data/userid/webice/image. For example, if joeuser analyzes inf_1_001.img, output files inf_1_001.log and inf_1_001.spt.img will be saved in the
/data/joeuser/webice/image directory.


Technical questions: Webmaster    Content questions: Ana Gonzalez

Last modified:Tuesday, 13-Aug-2019 14:45:10 PDT.