OSIRIX (“THE SOFTWARE”) IS PROVIDED AS IS. USE THE SOFTWARE AT YOUR OWN RISK. THE AUTHORS MAKE NO WARRANTIES AS TO PERFORMANCE OR FITNESS FOR A PARTICULAR PURPOSE, OR ANY OTHER WARRANTIES WHETHER EXPRESSED OR IMPLIED. NO ORAL OR WRITTEN COMMUNICATION FROM OR INFORMATION PROVIDED BY THE AUTHORS SHALL CREATE A WARRANTY. UNDER NO CIRCUMSTANCES SHALL THE AUTHORS BE LIABLE FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES RESULTING FROM THE USE, MISUSE, OR INABILITY TO USE THE SOFTWARE, EVEN IF THE AUTHOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. THESE EXCLUSIONS AND LIMITATIONS MAY NOT APPLY IN ALL JURISDICTIONS. YOU MAY HAVE ADDITIONAL RIGHTS AND SOME OF THESE LIMITATIONS MAY NOT APPLY TO YOU.
Data Reduction Pipeline - Due to the unique nature of OSIRIS data and of its calibration steps, the OSIRIS team has developed a comprehensive pipeline designed to fully reduce all of the calibration data and to reduce scientific data to the level where an astronomer can begin custom analysis. The OSIRIS pipeline is designed to fix artifacts on the raw 2D array, wavelength calibrate, and assemble all the spectra into a 3D cube (λ wavelength, x and y spatially). In addition, after the 3D cube is assembled the pipeline allows for mosaicking of multiple frames with integer lenslet steps. The OSIRIS team is continually optimizing the pipeline and analysis tools for all users. However, unlike space-based data reduction pipelines, the general user is responsible for generating their own custom analysis tools for their specific scientific project. The OSIRIS team and other users have been developing stand alone analysis tools. We highly recommend and support a cohesive community for OSIRIS data reductions and analysis. Please see the OSIRIS manual for detailed instructions on how to install and run the data reduction pipeline.![Osiris machete Osiris machete](https://static.giantbomb.com/uploads/original/1/13239/463775-chris_penn1_98683a.jpg)
Data Reduction GUI - The pipeline accepts commands only from XML (eXtensible Markup Language) files that we refer to as data reduction files (DRFs). Users may either hand edit these DRFs or use the java ODRFGUI package which generates DRFs with the user specifications. This GUI allows users to easily select pipeline modules, input directories, output directories, and execute scripts into the pipeline. This GUI should onlybe used with the version 2.0 or higher of the pipeline, and requires java 1.4 or higher. To use, download and unpack the package and consult the README file.
OSIRIS Updates - This website lists all the major hardware and software changes, and information on the calibration scans for OSIRIS. The pipeline uses a calibration scan for each independent mode (combination of filter and scale) to determine the spectral extraction and wavelength solution. Please use this page to determine which calibration scans you should be using for your observations.
![Osiris For Mac Osiris For Mac](/uploads/1/3/4/7/134799151/346986757.png)
If your OSIRIS paper is not represented here, please contact the with your paper details.
. Mac OS X 10.2 (Jaguar). Thoth or MT-Newswatcher for OS X. You must have either Thoth or MT-Newswatcher open before launching Osiris, and have your newsreader configured properly. Osiris is fairly self-explanatory. The OSIRIS software has been designed as a general medical image manipulation and analysis software. The design is mainly based on the following criteria.
THIS SOFTWARE IS NOT INTENDED FOR PRIMARY DIAGNOSTIC, ONLY FOR SCIENTIFIC USAGE.
THIS VERSION OF OSIRIX IS NOT CERTIFIED AS A MEDICAL DEVICE FOR PRIMARY DIAGNOSIS. THERE ARE NO CERTIFICATIONS. YOU CAN ONLY USE OSIRIX AS A REVIEWING AND SCIENTIFIC SOFTWARE, NOT FOR PRIMARY DIAGNOSTIC.
CERTIFIED VERSION OF OSIRIX IS AVAILABLE HERE: OSIRIX MD
All calculations, measurements and images provided by this software are intended only for scientific research. Any other use is entirely at the discretion and risk of the user. If you do use this software for scientific research please give appropriate credit in publications. This software may not be redistributed, sold or commercially used in any other way without prior approval of the author.
OSIRIS
OH-Suppressing Infra-Red Imaging SpectrographPI: James Larkin (UCLA) Project Scientist: Andreas Quirrenbach (UCSD) Co-PI: Alfred Krabbe (UC Berkeley) |
NOTE: The Keck OSIRIS Toolbox now has latest version of the OSIRIS pipeline.
Overview
OSIRIS is an integral field spectrograph designed to work with theKeck Adaptive Optics System. It uses an array of tiny lenses to samplea rectangular patch of the focal plane and produces spectra at up to3000 locations simultaneously. There is also an internal diffractionlimited camera with a 20x20 arcsec field of view. Both the camera andspectrograph can operate at wavelengths between 1 and 2.4 microns. Thecenter of the imaging camera’s field is about 20 arcsec offsetfrom the center of the spectrograph field and both can be usedsimultaneously with the same or different filters.
The spectrograph has plate scales of 0.02, 0.035, 0.05 and 0.10arcsec per lenslet. The spectral resolution averages 3800 in the threefinest plate scales, but is closer to 3400 in the 0.100 arcsec platescale. In the broadband mode each spectrum contains a full broad band(z, J, H or K) and a total of 16x64 (actually 1019) spectra aretaken. In the narrowband mode, a typical spectrum contains 1/4th of abroad band and an individual exposure contains between 16x64 to 48x64spectra depending on the exact filter selected. The imager has asingle fixed plate scale of 0.020 arcsec per pixel.
A great deal of thought has gone into trying to make OSIRIS easy touse. For the spectrograph, the only user selectable items are theplate scale, the filter, and the exposure time. The imager only has afilter and an exposure time setting. A great deal of complexity,however, is allowed in the observing sequences and the slaving of theimager to the spectrograph. All setup and control aspects of theinstrument are managed by a few GUIs.
There is also a data reduction system that includes a“real-time” reduction of raw frames into cubes for displayand basic analysis. In this real-time mode, it takes about one minutefor a preliminary data cube to appear in the “quicklook”display package. The reduction system also includes a growing set offinal reduction steps including correction of telluric absorption andmosaicing of multiple cubes.
Osiris Macdonald
First light was obtained on February 22, 2005 - See OSIRIS 1st Light Pictures!
The OSIRIS Toolbox
NOTE: Keck has become the primary distributor of the OSIRIS Data Reduction Pipeline. Some of the following information and files have been redirected to Keck! Please access the new OSIRIS Toolbox at this link: http://www2.keck.hawaii.edu/inst/osiris/tools/
The OSIRIS team and Keck staff would like to help OSIRIS users achieve a successful and rewarding observing experience! OSIRIS is an innovative and unique spectrograph, and hence it takes more preparation than traditional spectrographs with planning and reductions. We suggest looking over the OSIRIS manual prior to your observing run as well as the Keck OSIRIS webpage for further telescope and AO information. We have included links to the packages you will need for pre-observing (manual and planning GUI) and post-observing (Quicklook2 and data reduction pipeline).
OSIRIS User's Manual (pdf) - (v4.2 05/07/2018) Please refer to the OSIRIS manual for a complete description of OSIRIS capabilities, observational procedures, data reduction system, detector performance, filter curves, and much more.
OSIRIS Software Github - The OSIRIS software is now hosted on github. Historical descriptions are listed below.
Observing Planning GUI - OSIRIS observers can generate and save planning scripts, data definition files (.ddf), for observing with the spectrograph and imager by using the Observing Planning GUI. This java package will be identical to what you will be using at the telescope and requires java 1.4 or higher. To use, download and unpack the package and refer to the README file.
Quicklook2 Package - OSIRIS spectrograph frames are 3D FITS files that require sophisticated image visualization tools. The OSIRIS team presents an IDL based software package called Quicklook to display and analyze your OSIRIS data cubes. Quicklook is the OSIRIS image analysis software used at Keck while observing, but we also encourage using Quicklook for post-observing analysis of 2-D and 3-D fits frames. To use, simply download the tar file and unpack the file somewhere in your IDL path. Edit the environment variable 'QL_FILEDIR' in the file 'run_ql2' to match the directory path where you just unpacked Quicklook2.tar file. Once this environment variable has the correct path, you are ready to start using Quicklook2. Type 'run_ql2' at your terminal prompt within the same directory, and this script should launch Quicklook2 program and place the IDL xterm in an icon. In Windows, type 'run_wql2' at the IDL prompt. This software package supports the UNIX, LINUX, Mac OS, and Windows operating systems and operates on IDL versions 5.4 or higher.
Observing Planning GUI - OSIRIS observers can generate and save planning scripts, data definition files (.ddf), for observing with the spectrograph and imager by using the Observing Planning GUI. This java package will be identical to what you will be using at the telescope and requires java 1.4 or higher. To use, download and unpack the package and refer to the README file.
Quicklook2 Package - OSIRIS spectrograph frames are 3D FITS files that require sophisticated image visualization tools. The OSIRIS team presents an IDL based software package called Quicklook to display and analyze your OSIRIS data cubes. Quicklook is the OSIRIS image analysis software used at Keck while observing, but we also encourage using Quicklook for post-observing analysis of 2-D and 3-D fits frames. To use, simply download the tar file and unpack the file somewhere in your IDL path. Edit the environment variable 'QL_FILEDIR' in the file 'run_ql2' to match the directory path where you just unpacked Quicklook2.tar file. Once this environment variable has the correct path, you are ready to start using Quicklook2. Type 'run_ql2' at your terminal prompt within the same directory, and this script should launch Quicklook2 program and place the IDL xterm in an icon. In Windows, type 'run_wql2' at the IDL prompt. This software package supports the UNIX, LINUX, Mac OS, and Windows operating systems and operates on IDL versions 5.4 or higher.
- You may download example reduced OSIRIS cubes (broadband and narrowband) of star HD106965 for interacting with Quicklook2 -
OSIRIS Cube Kbb 0.1' and OSIRIS Cube Jn3 0.1'
Data Reduction Pipeline - Due to the unique nature of OSIRIS data and of its calibration steps, the OSIRIS team has developed a comprehensive pipeline designed to fully reduce all of the calibration data and to reduce scientific data to the level where an astronomer can begin custom analysis. The OSIRIS pipeline is designed to fix artifacts on the raw 2D array, wavelength calibrate, and assemble all the spectra into a 3D cube (λ wavelength, x and y spatially). In addition, after the 3D cube is assembled the pipeline allows for mosaicking of multiple frames with integer lenslet steps. The OSIRIS team is continually optimizing the pipeline and analysis tools for all users. However, unlike space-based data reduction pipelines, the general user is responsible for generating their own custom analysis tools for their specific scientific project. The OSIRIS team and other users have been developing stand alone analysis tools. We highly recommend and support a cohesive community for OSIRIS data reductions and analysis. Please see the OSIRIS manual for detailed instructions on how to install and run the data reduction pipeline.
![Osiris machete Osiris machete](https://static.giantbomb.com/uploads/original/1/13239/463775-chris_penn1_98683a.jpg)
Data Reduction GUI - The pipeline accepts commands only from XML (eXtensible Markup Language) files that we refer to as data reduction files (DRFs). Users may either hand edit these DRFs or use the java ODRFGUI package which generates DRFs with the user specifications. This GUI allows users to easily select pipeline modules, input directories, output directories, and execute scripts into the pipeline. This GUI should onlybe used with the version 2.0 or higher of the pipeline, and requires java 1.4 or higher. To use, download and unpack the package and consult the README file.
OSIRIS Updates - This website lists all the major hardware and software changes, and information on the calibration scans for OSIRIS. The pipeline uses a calibration scan for each independent mode (combination of filter and scale) to determine the spectral extraction and wavelength solution. Please use this page to determine which calibration scans you should be using for your observations.
OSIRIS Team
The OSIRIS team would prefer the following reference to be citedwhen referring to the instrument in publication:
'OSIRIS: a diffraction limited integral field spectrograph for Keck'
Larkin et al. 2006, Proceedings of the SPIE, Volume 6269, pp. 62691A (2006)
'OSIRIS: a diffraction limited integral field spectrograph for Keck'
Larkin et al. 2006, Proceedings of the SPIE, Volume 6269, pp. 62691A (2006)
OSIRIS Engineering Team: James Larkin, Matthew Barczys,Alfred Krabbe, Sean Adkins, Ted Aliado, Paola Amico, George Brims,Randy Campbell, John Canfield, Thomas Gasaway, Allan Honey, ChristofIserlohe, Chris Johnson, Evan Kress, David Lafreniere, Ken Magnone,Nick Magnone, Michael McElwain, Juleen Moon, Andreas Quirrenbach,Gunnar Skulason, Inseok Song, Michael Spencer, Jason Weiss, andShelley Wright
OSIRIS Commissioning Team: James Larkin, Matthew Barczys, Alfred Krabbe, Christof Iserlohe, Michael McElwain, Andreas Quierrenbach, Jason Weiss, and Shelley Wright
OSIRIS Keck Support Team: Jim Lyke, Randy Campbell, and Al Conrad
OSIRIS Data Reduction Pipeline Team: James Larkin, Shelley Wright, Jason Weiss, Mike McElwain, Marshall Perrin, Christof Iserlohe, Alfred Krabbe, Tom Gasaway, and Tommer Wizanski
OSIRIS Quicklook2 Package: Michael McElwain, Jason Weiss, Marshall Perrin, and James Larkin
OSIRIS Science Publications
(25 papers and running...)
'Diffraction-limited Imaging Spectroscopy of the Sagittarius A* Region Using OSIRIS, a New Keck Instrument'
Krabbe et al. 2006, ApJL, Volume 642, Issue 2, pp. L145-L148
Krabbe et al. 2006, ApJL, Volume 642, Issue 2, pp. L145-L148
'First High-Contrast Science with an Integral Field Spectrograph: The Substellar Companion to GQ Lupi'
McElwain et al. 2007, ApJ, Volume 656, Issue 1, pp. 505-514
McElwain et al. 2007, ApJ, Volume 656, Issue 1, pp. 505-514
'Integral Field Spectroscopy of a Candidate Disk Galaxy at z ~ 1.5 Using Laser Guide Star Adaptive Optics'
Wright et al. 2007, ApJ, Volume 658, Issue 1, pp. 78-84
Wright et al. 2007, ApJ, Volume 658, Issue 1, pp. 78-84
'Laser Guide Star Adaptive Optics Integral Field Spectroscopy of a Tightly Collimated Bipolar Jet from the Herbig Ae Star LkHα 233'
Perrin & Graham 2007, ApJ, 670, 499
Perrin & Graham 2007, ApJ, 670, 499
'Tvashtar awakening detected in April 2006 with OSIRIS at the W.M. Keck Observatory'
Laver, de Pater, & Marchis 2007, Icarus, 191, 749
Laver, de Pater, & Marchis 2007, Icarus, 191, 749
'Widespread Morning Drizzle on Titan'
Ádámkovics et al. 2007, Science, 318, 5852, 962
Ádámkovics et al. 2007, Science, 318, 5852, 962
'Integral Field Spectroscopy of High-Redshift Star Forming Galaxies with Laser Guided Adaptive Optics: Evidence for Dispersion-Dominated Kinematics'
Law et al. 2007, ApJ, 669, 929
Law et al. 2007, ApJ, 669, 929
'High-contrast imaging with Keck adaptive optics and OSIRIS'
McElwain et al. 2008, SPIE, 7015
McElwain et al. 2008, SPIE, 7015
'A Near-Infrared Variability Study of the Galactic Black Hole: A Red Noise Source with NO Detected Periodicity'
Do et al. 2009, ApJ, 691, 1021
Do et al. 2009, ApJ, 691, 1021
'The Role of Molecular Gas in Obscuring Seyfert Active Galactic Nuclei'
Hicks et al. 2009, ApJ, 696, 448
Hicks et al. 2009, ApJ, 696, 448
'The Kiloparsec-Scale Kinematics of High-Redshift Star-Forming Galaxies'
Law et al. 2009, ApJ, 697, 2057
Law et al. 2009, ApJ, 697, 2057
Osiris Software For Mac
'Dynamics of Galactic Disks and Mergers at z~1.6: Spatially Resolved Spectroscopy with Keck Laser Guide Star Adaptive Optics'
Wright et al. 2009, ApJ, 699, 421
Wright et al. 2009, ApJ, 699, 421
'An OSIRIS Study of the Gas Kinematics in a Sample of UV-Selected Galaxies: Evidence of 'Hot and Bothered' Starbursts in the Local Universe'
Basu-Zych et al. 2009, ApJL, 699, L118
Basu-Zych et al. 2009, ApJL, 699, L118
![Osiris For Mac Osiris For Mac](/uploads/1/3/4/7/134799151/346986757.png)
'The global distribution of sulfur dioxide ice on Io, observed with OSIRIS on the W.M. Keck telescope'
Laver & de Pater 2009, Icarus, 201, 72
Laver & de Pater 2009, Icarus, 201, 72
'Component-resolved Near-infrared Spectra of the (22) Kalliope System'
Laver et al. 2009, Icarus, 204, 574
Laver et al. 2009, Icarus, 204, 574
'Probing young massive clusters with laser guide star adaptive optics'
McCrady, N. 2009, ApSS, 324,109
McCrady, N. 2009, ApSS, 324,109
'Evidence for strong dynamical evolution in disc galaxies through the last 11 Gyr. GHASP VIII - a local reference sample of rotating disc galaxies for high-redshift studies'
Epinat et al. 2010, MNRAS, 401, 2113
Epinat et al. 2010, MNRAS, 401, 2113
'The Presence of Weak Active Galactic Nuclei in High Redshift Star Forming Galaxies'
Wright et al. 2010, ApJ, 711, 1291
Wright et al. 2010, ApJ, 711, 1291
'Resolved spectroscopy of gravitationally lensed galaxies: recovering coherent velocity fields in subluminous z ~ 2-3 galaxies'
Jones et al. 2010, MNRAS, 369
Jones et al. 2010, MNRAS, 369
'Discovery of a Young L Dwarf Binary, SDSS J224953.47+004404.6AB'
Allers et al. 2010, ApJ, 715, 561 (using OSIRIS Imager)
Allers et al. 2010, ApJ, 715, 561 (using OSIRIS Imager)
'The Lick AGN Monitoring Project: The MBH - sigma Relation For Reverberation-Mapped Active Galaxies'
Woo et al. 2010, ApJ, 716, 269
Woo et al. 2010, ApJ, 716, 269
'The 2008 Outburst in the Young Stellar System Z CMa: The First Detection of Twin Jets'
Whelan et al. 2010, ApJ, 720L, 119W
Whelan et al. 2010, ApJ, 720L, 119W
'Near-infrared Spectroscopy of the Extrasolar Planet HR 8799 b'
Bowler et al. 2010, ApJ, 723, 850
Bowler et al. 2010, ApJ, 723, 850
'The Black Hole Mass in Brightest Cluster Galaxy NGC 6086'
McConnell et al. 2010, arxiv:1009.0750 U
McConnell et al. 2010, arxiv:1009.0750 U
'Measurement of a Metallicity Gradient in a z=2 Galaxy: Implications for Inside-Out Assembly Histories'
Jones, Ellis, Jullo, & Richard 2010, arxiv:1010.1538
Jones, Ellis, Jullo, & Richard 2010, arxiv:1010.1538
'Clouds and Chemistry in the Atmosphere of Extrasolar Planet HR8799b'
Barman, Macintosh, Konopacky, Marois 2011, arxiv:1103.3895
Barman, Macintosh, Konopacky, Marois 2011, arxiv:1103.3895
'The Nature of Double-peaked [O III] Active Galactic Nuclei'
Fu, Hai; Yan, Lin; Myers, Adam D.; Stockton, Alan; Djorgovski, S. G.; Aldering, G.; Rich, Jeffrey A, ApJ, 745, 67F
Fu, Hai; Yan, Lin; Myers, Adam D.; Stockton, Alan; Djorgovski, S. G.; Aldering, G.; Rich, Jeffrey A, ApJ, 745, 67F