Chris Griffith

Document Sample
Chris Griffith Powered By Docstoc
					                   February 16, 2010
Chris
Griffith           EVOSTA
Interviews 1 & 3                       IST 420
Table of Contents
EVOSTA Project Background .................................................................................................... 3
   Main Processes ...................................................................................................................... 3
Pre-Scan .................................................................................................................................... 4
   Intro ........................................................................................................................................ 4
   Pre-Scanning.......................................................................................................................... 4
      Mice .................................................................................................................................... 4
      Baboons ............................................................................................................................. 4
   Explanation ............................................................................................................................ 4
HRCT Scan................................................................................................................................ 5
   Scanning Process .................................................................................................................. 5
   Explanation ............................................................................................................................ 6
Processing ................................................................................................................................. 7
   Lab ......................................................................................................................................... 7
   Explanation ............................................................................................................................ 7
Data Retrieval ............................................................................................................................ 8
   Archive Retrieval .................................................................................................................... 8
   Explanation ............................................................................................................................ 8
Overview .................................................................................................................................... 9
Key Organizations and Terms .................................................................................................... 9
      CAT .................................................................................................................................... 9
      CQI ..................................................................................................................................... 9
      GWU ...................................................................................Error! Bookmark not defined.8
      HRCT.................................................................................................................................. 9
      NSF .................................................................................................................................... 9
EVOSTA Project Background
 A research project funded by the National Science Foundation, set to examine the genetics that
determine facial development in humans and how have changed through evolution. The main
aid to this project is the HRCT located inside CQI's headquarters at Penn State. This scanner is
used for multiple projects and is a service available to anyone. The scanner is recommended
only for small and/or precise and /or precious objects.

Main Processes



              • Manage the baboon and mice colonies
              • Prepare skulls for scanning from Washington University
 Pre-Scan


              • Calibrate the High Resolution Computed Tomography (HRCT)
              • Scan Data
   HRCT       • Send to RAID Array
   Scan       • Archive Data



              • Transfer data to Dr. Rchmyer's Lab
              • Process the Images
Processing    • Analyze the data




              • Request archived data and receive approval
   Data       • Find and send data to requestor
  Retrieval
Pre-Scan
Intro
To have continuous data for research, farms of animals must be kept intact with the same
bloodlines. This enables tracking changes in evolution over time. For all data scanned for the
HRCT is mice that are kept by Washington University. The NSF also manages a baboon colony,
but they are scanned by Medical CAT Scanners instead.

Pre-Scanning
Mice

                                   Post-                                      Data
              Mice                mortem                Skulls              stored on
            breed in                                    sent to
                                    skull                CQI                incoming
            captivity
                                  retrieval                                   skulls


Baboons


          Baboon's                                                          Data sent to
                              Post-mortem            Skulls sent to
            family                                                              Dr.
                                                     Washington
          structure           skull retrieval                               Rchmyer's
                                                      University
          recorded                                                              Lab


Explanation
       Breeding Animals
           o The animals are first studied while alive to track changes in behavior or family
               structure. Also any noticeable physical features differences or other auspicious
               mutations are recorded.
       Dissecting for Skulls
           o After the death of the animal, they are dissected and the skulls are retrieved.
       Packaging
           o Once cleaned and polished, the skulls are packaged. They are sent to their
               designated scanning facility.
       Aggregate Data
           o Depending on where the item was sent, the item may be scanned elsewhere,
               and the data brought into the Lab, or simply sent to Penn State where the high
               resolution scan will be preformed.
HRCT Scan
Scanning Process


                                      Request Scans

  Complete Request Forms      Officalize Payment Method         Send Specimn to Scanner



                                    Calibrate Scanner

          Seven Tests Performed                     Images Reviewed For Quality Control



                                      Record Settings
                                               Some Settings Saved as Metadata with the
       Settings Recorded to Notbook
                                                             TIF images



                                         Scan it!




                                   Store Scanner Data

       Data Streamed to Workstation             Split into Second Workstation via Ethernet



                                  Send Data Researchers

          Transfer Thorugh FTP                                   Mail DVD



                                       Archive Data

    Manually Send Images to RAID Array                Backup Important info on Tapes




                                       Return Bones
Explanation
      Request from Washington University for Mice Skull Scan
           o Washington University asks for a new batch of skulls to be examined. This is
               usually done with personal contact or through email.
      Sending the bones to CQI's HRCT
           o Washington University has now gone through the pre-scanning process and has
               the bones shipped to the HRCT at Penn State.
      Prepare bones for scan
           o Align mouse skulls so they are able to scan three at a time. Align them in
               columns and mount them on glass pikes.
      Calibrate Scanner
           o One of the more tedious processes, the scanner is calibrated by hand. All the
               settings are then recorded in a notebook alone with the skull data.
      Scan it!
           o That's right, it's now time to rev up the HRCT and see what it can do. It will take
               image slices that are only 5 microns apart.
      Store the data
           o The data is then stored on a RAID array of hard drives that are mirrored which
               consist of about 9 terabytes of total space, of which 4.5 can be utilized.
      Send data to lab
           o All this data is then sent via DVD or FTP to the lab for analysis.
      Archive data
           o The data is then recorded off of them on 200 gigabyte tape drives.
      Return the Bones
           o Running out of storage room as is, CQI sends the skulls back after the
               appropriate data is retrieved.
Processing
Lab

  Send Image data to   Split Images by   Aggregate Images of
                                                               Render as 3D model   Analyze 3D mutations
         Lab              Columns         Same Specimen




Explanation


      Retrieve data from HRCT
           o The data has now been sent from the HRCT to the lab in Image form.
      Splitting images
           o Graduate students spend the very tedious time of splitting the images up into the
               three different images that the mice were in. This has to be done so each image
               only has a single mouse head in 3D view. This is done with a program called
               Image J.
      Aggregate Images
           o Now that the images are the same specimen, they need to be ordered and
               grouped and layered to produce a 3D image.
      Render as 3D model
           o The images are now layered and are displayed in a special program that will
               show them as 3D models. These are highly detailed and specific points or areas
               can be marked or flagged.
      Analyze 3D mutations
           o More tedious work, find the locations of several key points that denote key
               feature of an animal's skull. Then notice the difference is both size and percent
               distance change between points relative to the size of the skull.
Data Retrieval
Archive Retrieval




                                                            Send
                                              Copy Data     Media to
                                              to Media      Requestor
                                Find
                                Location of
                                Data
                      Approve
                      Request

           Request
           for Data




Explanation


      Request data
          o When an area loses data and needs another copy, or another researcher wants
               access to the images a request must be made. This is generally done through
               email but can also be less formal.
      Approve request
          o Penn State technically owns any and all data it scans. However, ethically the
               requestor needs to have permission from the owner of the object to retrieve and
               use a copy of it. The data will never be published without permission, but there
               are still unclear ethics.
      Find location of data
          o The data is either remembered where it was stored, or have to be searched
               through paper binders to find where they were saved.
      Copy data to media
          o The data is sent to the requestor by one of two methods. Tim is either able to set
               up an FTP server they can download it from or send them the image on a DVD
               format.
      Send media to Requestor
          o If the media is in DVD format, it needs to be sent to the requestor by mail. This
               may incur fees for the requestor.
Overview

Each activity plays a difference in importance role, but all are essential to get the job done. They
take various amount of time or resources and each play into a bigger role. Overall, there is a
clear pattern of how the operation works from the life of the animal to examining and comparing
it's skull to its ancestors. This project is helping take us further and closer to answering the
questions that previously could only be guessed.


Key Organizations and Terms

CAT - Computerized Axial Tomography Scanner

CQI - Center for Quantitative Imaging

HRCT - High Resolution Computed Tomography

NSF - National Southwest Foundation

				
DOCUMENT INFO
Shared By:
Categories:
Tags:
Stats:
views:4
posted:8/10/2011
language:English
pages:9