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Pitzer
WCStools is a program package designed for working with Images and the World Coordinate System. The aim of WCStools is to provide methods for relating pixels taken common astronomical images to sky coordinates.
Availability and Restrictions
The following versions of WCStools are available on OSC clusters:
Pitzer
Cell Ranger is a cell analysis library for generate feature-barcode matrices, perform Analysis for RNA samples. Cell Ranger works in pipelines for it's RNA sequencing analysis which allows it to: process raw sequencing output, read alignment, generate gene-cell matrices, and can perform downstream analyses such as clustering and gene expression analysis.
SUG Conference - October 7, 2021
Agenda
Gateway, Pitzer
Join a Classroom Project
Your classroom instructor will provide you with a project and access code that will allow you to join the classroom project. Visit our user management page for more information.
SUG Conference - April 14, 2021
Agenda
The data transfer speed between OSC and another network can be tested.
Test data transfer speed with iperf3 tool
Connect to a data mover host at osc and note the hostname.
$ ssh sftp.osc.edu # login $ hostname datamover02.hpc.osc.edu # the hostname may also be datamover01.hpc.osc.edu
From there, an iperf3 server process can be started. Note the port used.
Pitzer
Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurrig due to beam-induced motion. It reads stacks of movies that are stored in MRC/CCP4 format. Unblur generates frame sums that can be used in subsequent image processing steps and optionally applies an exposure-dependent filter to maximize the signal at all resolutions in the frame averages. Movie frame sums can also be calculated using Summovie, which uses the alignment resuls from a prior run of Unblur.
Pitzer
OpenCV is an open-source library that includes several hundreds of computer vision algorithms.
In December 2021 OSC updated its firewall to enhance security. As a result, SSH sessions are being closed more quickly than they used to be. It is very easy to modify your SSH options in the client you use to connect to OSC to keep your connection open.
In ~/.ssh/config (use the command touch ~/.ssh/config to create it if there is no exisitng one), you can set 3 options:
Pitzer
MotionCor2 uses multi-GPU acceleration to correct anisotropic cryo-electron microscopy images at the single pixel level across the whole frame, making it suitable for single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting.
Availability and Restrictions
Versions
The following versions are available on OSC clusters:
