Image Processing with Karst

Reo virus (spherical/icosahedral virus)

The initial collection of images of reovirus were obtained from Tim Baker's electron microscopy software collection as a test problem for processing frozen-hydrated images of reovirus using the auto3dem package. We have included the auto3dem test problem here, but have also added additional exercises with these images using EMAN.

P22 virus (spherical/icosahedral virus)

This small collection of images of P22 virus images were obtained from Tim Baker's electron microscopy software collection as an additional test problem for processing frozen-hydrated virus images using the auto3dem package. We have again included the auto3dem test problem here, but have also added additional exercises with these images using EMAN.

GroEL (d7 point group symmetry)

The images used in this demo have been reduced in size and imited to only 40,000 images. They were obtained during a collaboration with Brad Pesavento at the Lawrence Livermore National Lab (LLNL). The images were recorded at the National Resource for Automated Molecular Microscopy (NRAMM), part of the Center for Integrative Molecular Biosciences (CIMB) at the Scripps Research Institute (TSRI) in San Diego, and have been used both here at IU and at LLNL as test data sets for massively parallel computer clusters.

Ribosomes (asymmetric particle)

One set of images was recorded onto film (and then scanned) as part of a project in the laboratory of Chris Akey at the Boston University School of Medicine, and resulted in a publication about eucaryotic ribosomes. The second data set comes from Joachim Frank's group and is part of the published tutorial described in more detail within this data set.

auto3dem

Using the auto3dem Package on the IUB Clusters

EMAN1

Using the EMAN Packages on the IUB Clusters

EMAN2

Using the EMAN2 Packages on the IUB Clusters

frealign

Using the frealign Packages on the IUB Clusters

Relion

Using the Relion Packages on the IUB Clusters

SPARX

Using the SPARX Packages on the IUB Clusters

SPIDER

Using the SPIDER Packages on the IUB Clusters

XMIPP

Using the XMIPP Packages on the IUB Clusters