Q: What data format does the program
support
for image input?
A: MRC files for
both 2D
electron micrograph and 3D image stack. Signature is able to read TIFF and
SPIDER 2D
image, which can then be saved to an MRC file for
further processing. Notice that the batch processing function supports
MRC format only.
Q: What data format does the
program support for particle selection output?
A: For 2D coordinates, Signature supports PTK (a
proprietary format), PLT (IMAGIC format)
and SPD (SPIDER format). As for images, the selected particles can be
output to a 3D MRC stack.
Q: How to prepare template
images used in the algorithmic particle screening?
A: Template images should
be in the form of an MRC stack. They can be created in several ways: 1)
2D
projections from a low-resolution density model; 2) class averages from
a handful pre-selected particles; or, 3) images cropped from the given
micrograph (possibly after low-pass filtering to reduce noise).
Q: How to crop a rectangular
section from a
2D image?
A: An image cropping
function is
provided in 2D-Image
OpPanel. Place the mouse cursor at the region of interest,
press CTRL, click and drag the mouse left button. Upon mouse button
release, the selected section will be
displayed in the rectangular monitor in the panel. The cropped image
can be
saved to an MRC file (the Save
button under the monitor). One application of this cropping
function is to generate a set of templates directly from a given
micrograph and to proceed with automated particle screening.
Q: How to crop a filament
segment from a 2D image?
A: When the box by Filament
Boxing is checked, image can be cropped along any direction.
Place the mouse cursor at the region of interest,
press CTRL, click and drag the mouse left button. Upon mouse button
release, the selected section will be
displayed in the monitor. The image will have
been rotated to the horizontal orientation.
Q: A SPIDER particle
coordinates file does not match the micrograh display. Why?
A: The problem most
likely comes from image conversion: when a micrograph in SPIDER format
is converted to the MRC format, the conversion should be processed in
the SPIDER program. It is known that, if the IMAGIC program is
used, the output image will be flipped. Signature can read the particle
selection file originally generated by SPIDER and display it properly
on the micrograph, if the image format conversion is correct.
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