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Owens, Pitzer

CIAO (also known as Chandra Interactive Analysis of Observations) is a X-Ray telescope analysis software package for astronomical observation. CIAO focuses on the Chandra X-ray observatory. It contains a toolset used to analyze fits files and is commonly used in conjuction with DS9 and Sherpa, and focuses on data flexibility. 

DS9

Owens, Pitzer

SAOImageDS9 is a astronomical imaging and data visualization application. DS9 provides support for FITS images, binary tables, multiple frame buffers, region manipulation, and colormaps display options

Availability and Restrictions

The following versions of DS9 are available on OSC clusters:

Owens, 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.

Gateway, Owens, Pitzer

Add to a Classroom Project

We provide the instructor (PI of the classroom project) with information on how to get students added to the classroom project. Usually, invites will be sent to new OSC users; existing OSC users will be automatically added to the project if they have an OSC account which matches the email information provided by the PI.

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.

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