Web is a graphical user interface for displaying
and interacting with SPIDER
format images. It was developed at the
Wadsworth Center in
Albany, New York.
Web is written in "C" and runs under X-Window/Motif.
Web was developed by
with contributions from L. Odesanya, Y.H. Li, M. Ladjadj, A. Dent,
P. Penczek, and
X-Window/Motif Web has been in use since 1990 and contains
50,000 lines of code.
A Java based Web with fewer operations,
written by Bimal Rath, is also available for use on
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. |
|COMMANDS||Operations 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
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!)
Enhances contrast of image using thresholding.
Selects cursor style from a pallette.
Turns off scrolling text window.
- Selects font for drawing text.
Sets magnification area and magnification factor.
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)
Shows an image. Will try to place the image
on the screen so that it does not overlap previous images.
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
Use the movie toggle in the Image Option menu to force all
images to be displayed at the same location.
- 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.
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.
Pans previously displayed image within its original
display area. Can be used for images too large for the Web
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.
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.
- 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
Does some discrete
convolutions on an image.
Displays correspondance map. Can
then outline areas and query images found within areas.
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.
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
- 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.
Draws image histogram on screen.
Interactively magnifies an area of the screen.
Interactively selects marker
locations and stores locations relative to image in a SPIDER
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
Displays a movie from a series of images.
- 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.
- CTF from Document file
Interactively study CTF plot.
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!
Displays the profile of image intensities along a row
Interactively picks reflections from a
diffraction pattern and places indices and locations in
a document file.
Creates and displays a "single image
relative displacement stereogram" from a volume.
Draws horizontal or vertical bars on screen
using previously set foreground color.
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
Draws lines on screen using previously set foreground color.
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.
- 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
Stops Web and closes Web window.