JWeb for Linux

Web is a graphical user interface for displaying and interacting with SPIDER format images. It contains more than 50,000 lines of "C" code, running under X-Windows/Motif, and has been in use since 1990. It was developed at the Wadsworth Center in Albany, New York by ArDean Leith with contributions from: L. Odesanya, Y.H. Li, M. Ladjadj, A. Dent, M. Radermacher, P. Penczek, J. Frank, and J. Bollinger.


Certain variables in Web can be initialized from Command Line Arguments or in your Xt Resource files.

Operations are grouped under five main menu headings:

OPTIONS Alter the way information is displayed during a session.
COMMANDSOperations which display or analyze 2D or 3D images.
EDIT Operations which edit 2D or 3D images.
INFO Information on workstation and Web capabilities.
SYSTEM Settings for file names and for exiting the application

Additionally the main menu has an area for often used operations:

IMAGE Display image/volume
CLEAR Clear images
EXIT Exit Web
CONTRAST Set contrast
SCALING Set image scaling (size)

Operations are selected by pointing at the relevant menu heading and then selecting the menu sub-option (and sub-sub-option) using the left mouse button.

    • Image
      Alters image display charactaristics:
      • Left & top margin around image display area
      • X & Y margin around each image
      • Size reduction for image display (-2 is a magnification of 2X)
      • Montage movie flag (keeps next image in same location as current image)
      • List file names below images
      • Start new row or screen of images
      • Toggle for listing files in file-selector (toggle off if you have hundreds of files!)
    • Contrast
      Enhances contrast of image using thresholding.
    • Cursor
      Selects cursor style from a pallette.
    • Display
      Turns off scrolling text window.
    • Font
    • Selects font for drawing text.
    • Magnify
      Sets magnification area and magnification factor.
    • Color
      Selects color for graphics characteristics:
      Foreground Color for graphics lines, text, etc.
      Background Color for image & graphics surround
      Overlay Color for Overlay (masking)
      Cursor Color for cursor
      Cursor outline Color for cursor border
    • Line Style
      Alters line style (in some operations)
    • Line Width
      Alters line width (in some operations)
    • Clear
      Clears screen.
    • Image
      Shows an image. Will try to place the image on the screen so that it does not overlap previous images.
    • Montage
      Shows a montage of 2-D images or 3-D slices or a stack. For 3-D slices the first slice in the file is z = 1 (a right-handed coordinate system).
      • x-slices have y-axis horizontal (y=1 at left) and z-axis vertical (z=1 at top), starting with x = 1.
      • y-slices have x-axis horizontal (x=1 at left) and z-axis vertical (z=1 at top), starting with y = 1.
      • z-slices have x-axis horizontal (x=1 at left) and y-axis vertical (y=1 at top), starting with z = 1.
      Use the movie toggle in the Image Option menu to force all images to be displayed at the same location.
    • Surface
      Does a fast surface display from a 3D file. User can specify surface level (threshold), contribution from depth versus surface reflectivity, scaling, and rotation. A movie option creates frames of a rotation sequence. Further details.
    • Shift
      Pans previously displayed image within its original display area. Can be used for images too large for the Web window.
    • Annotate
      Draws circles and numerical labels on top of an image. Positions for circles and values for labels are read from a SPIDER document file. User can specify registers for x & y coordinates and label.
    • Categorize
      Displays montage of individule or stacked images. Asks for new SPIDER document file name. User can assign a category to each image using mouse to select images. The category is toggled using the middle mouse button. Categories and file numbers are stored in a document file. Further details.
    • Colored Surface
      Does fast surface display of 3D file. Colors surface according to values found in a second 3D file. Specify surface level, contribution from depth and surface reflectivity, and number of colors. The values in the color volume are divided into the specified number of colors. A private color-map can be used to alter the correspondence between colors and intensities in the color volume. Can only handle less than six colors. Further details.
    • Convolve
      Does some discrete convolutions on an image.
    • Corr-map
      Displays correspondance map. Can then outline areas and query images found within areas. Further details.
    • Dendrogram
      Performs a "dendrogram" plot with input taken from a SPIDER CL CLA operation document file. Can also display the averaged images of a given threshold setting.
    • Distance
      Interactively queries a pair of pixel locations to determine their separation distance. Can record distances in a document file. Can record up to six distances from each starting point on a line of the document file.
    • General filter
      Interactively masks a power spectrum image to create a general Fourier filter. This filter file can then be multipled by a Fourier file for filtering. The mask is Gaussian and the radius can be specified. Further details.
    • Histogram
      Draws image histogram on screen.
    • Magnify
      Interactively magnifies an area of the screen.
    • Markers
      Interactively selects marker locations and stores locations relative to image in a SPIDER document file. Further details.
    • Mask
      Interactively draws polygons on screen to make a binary mask image. The mask image is stored in a file. This mask file can then be used in SPIDER for masking a grey scale image by multiplication. Will fail if the file to be masked is larger than window.
    • Montage from doc. file
      Makes a montage of individule or stacked 2-D images by looking up the image numbers in a document file. The image numbers must be in the first register (not keys) in the document file. All images must have same prefix in their name (e.g. IMA***.DAT). Further details.
    • Movie
      Displays a movie from a series of images. Further details.
    • Tilted Particles
      Interactively selects coordinates from an untilted/tilted pair of micrographs, determines tilt angle and tilt-axis direction by a least-square fit of all selected particle locations. Further details.
    • CTF from Document file
      Interactively study CTF plot. Further details.
    • Pixel
      Queries a pixel for location and color. Can place pixel location, color index value, in a document file.
    • Pixel within
      Queries a pixel for location within image, screen intensity, and pixels intensity in file. Can these values in a document file. Also used for interactive particle selection.
    • Power Spectrum
      Shows a power spectrum of enclosed area in a user drawn window. The spectrum is from screen data not file data. Does not work properly for some window sizes!
    • Profile
      Displays the profile of image intensities along a row or column. Further details.
    • Reflections
      Interactively picks reflections from a diffraction pattern and places indices and locations in a document file.
    • SIRDS
      Creates and displays a "single image relative displacement stereogram" from a volume.
  • EDIT
    • Bars
      Draws horizontal or vertical bars on screen using previously set foreground color.
    • Drill-n-fill
      Interactively edits a volume while viewing a surface view of volume. Volume is viewed along X axis. Surface view is same as surface operation. Mouse buttons control movement of a tool which drills or fills areas of the volume. Further details.
    • Lines
      Draws lines on screen using previously set foreground color.
    • Text
      Draws text on screen using previously set foreground color.
    • Draw Boxes
      Draws boxes on screen using previously set foreground color.
    • Move Area
      Moves or copies an area of the screen from one position to another. Useful also for editing labels, etc. for photography.
    • Window Last File
      Interactively windows a displayed file and saves window from original file in a new SPIDER image file.
  • INFO
    • X info
      Prints some debugging information in terminal window.
    • File Extension
      Sets extension to associate with file names e.g. DAT
    • Current Directory
      Sets current working directory. File searches begin from here.
    • File Pattern
      Selects pattern to use in searching for files eg. T*ST**0
    • EXIT
      Stops Web and closes Web window.

Source: web.html     Last update: 12/14/2018