Python Tools for SPIDER


These tools supplement the standard SPIDER visualization modules:
     WEB -- the classic image viewer for SPIDER
     JWeb -- Java-powered, platform-independent version of WEB.


The SPIDER Python Tools require their own installation which loads an appropriate version of Python and needed Python libraries.

Image viewers

qview.py
A quick Spider image viewer, for applications that need to display images

montage.py
View a montage of images.

montagefromdoc.py
View a montage of images selected by a SPIDER doc file.

viewstack.py
View images in a stack one-by-one.

classavg.py
View a montage of average images; clicking on any image brings up another montage of the image set of that average.

spiconvert.py
Convert SPIDER images to/from other formats.

Data plotting

scatter.py
Read a document file and display a scatterplot.

pyplot.py
Simple graphical interface to Gnuplot.

CTF tools

ctfmatch.py
A tool for analyzing the output from SPIDER's 'TF ED' command.

ctfdemo.py
Experiment with various CTF parameters used in SPIDER

ctfgroup.py
Assign micrographs to defocus groups.

ctfcircle.py
A dumb thing that puts a circle over a power spectrum

Other

verifybyview.py
Verify quality of particles.

xplor.py
Tree view of directory files

mkfilenums.py
List file numbers in SPIDER doc file.

xmippsel2spiderdoc.py
Convert a Xmipp sel file to a SPIDER doc file.

emancoords2spiderdoc.py
Convert EMAN coordinates file to a SPIDER doc file.