Center for Molecular and Genomic Imaging


Data Management

A CMGI relational database system is being developed in-house to manage the large amount of data generated routinely from multiple imaging modalities.  This system has several important features, including 1) a public application procedure to use our imaging services; 2) internal project management, e.g., approval/disapproval of submitted projects; collection of patient data records and images; time tracking for billing; session scheduling; data backup, archiving and planned disposal; 3) a secure data retrieval system, allowing researchers password-protected access  to their study data and images, which can be downloaded to their local computer;  and 4) a report system for CMGI administrators to generate summary reports of CMGI operations in order to evaluate overall Center performance, identify bottlenecks and estimate project costs.A digital patient data record (PDR) is a secured web application used to input key imaging session information, including a unique image session number, animal data (e.g., ID number, sex, weight), anesthesia information, and the scanning parameters relevant to each imaging modality. This information is input by CMGI staff, or by a trained member of the PI’s staff (termed the PDRUser) if the study is being conducted without CMGI staff assistance. Once entered, this data becomes a secure, permanent record that can be accessed only by authorized users.   Changes to a PDR can only be made by the PI’s appointed PDRUser(s) and CMGI staff.

Data backup and storage:

The highest priority is placed on organizing, securing and archiving data collected from each imaging modality.  Data handling/storage is modality dependent and data handling routines evolve as dictated by improvements in data processing software and data storage media.  We are currently working towards development of an automated data archiving system for all imaging modalities. When implemented, data will be automatically transferred to our current on-site server (2.2 TB RAID), which is mirrored at an external site (2.2 TB RAID) to provide redundant, secured imaging data.

PET:   The file types generated by PET imaging include list mode data (.lst), sinogram data (.scn), image data (.img) and text data (e.g, .hdr, .log).  Due to the large file sizes (GB) typical of list mode data, these files are routinely deleted after the sinogram files have been backed up.  An exception is made if the PI requests retention of .lst files for future reframing of their image data.  At the end of each day, sinogram, image and text files are zipped and backed up on our on-site server (2.2 TB RAID) and on a mirrored off-site server (2.2 TB RAID).   Data is also routinely archived on DVDs, and can be provided to PIs in this format by request.

Images reconstructed by the iterative MAP (maximum a posteriori) algorithm typically run after-hours and are not available to investigators until the next day.  CMGI staff upload image files to our server where they are password-protected and only available to the PI and members of the PI’s group.  Image files can be displayed and analyzed using MicroPET viewing software (ASIPro®) or other available software including AMIDE.  A copy of ASIPro can be provided to the PI for image viewing.

CT:  The acquired data files (.cat) are reconstructed into individual slices (.ct files), which can be converted to .am, and .raw file types for analysis by Amira® or AMIDE, respectively.  The .ct files can also be converted to dicom format.  All files are zipped and saved on an external hard drive, on our on-site server, and on the mirrored off-site server.

PET/CT:  For dual modality PET/CT imaging, we can provide the PI with coregistered datasets for image display in ASIPro or AMIDE.  The resliced CT data (.img file) is stored with the corresponding PET data, and the zipped files are burned to DVD and backed up on our on-site and mirrored off-site servers.

SPECT:  CMGI staff upload image files to our server where they are password-protected and only available to the PI and members of the PIs group.  Image files can be displayed and analyzed using MicroPET viewing software (ASIPro) or other available software including AMIDE.  A copy of ASIPro can be provided to the PI for image viewing.

MRI:  The raw data files acquired by MRI can be viewed with Bruker software (Paravision) or can be imported and viewed with various other viewing software, including AMIDE, Amira®, RView, or ASIPro (after further conversion in AMIDE).  Currently, the raw or dicom files are stored on the School of Medicine server, as well as on a CMGI staff computer and an external hard drive.  Periodically, files are archived to DVD.  MRI imaging is conducted on a Bruker Biospec 7T magnet at the adjacent NMR facility.  A new MRI imaging system to be located in the CMGI facility is anticipated in 2009.  Data storage and archiving for the new system will be processed within the CMGI at that time.

PET/MRI:  For dual modality PET/MRI imaging, we can provide the PI with coregistered datasets for image display in either ASIPro or RView.  These files are stored on a CMGI staff computer and an external hard drive, and are periodically archived to DVD.

Ultrasound:  Both cines and single image files can be stored on the host computer’s hard drive in dicom format.  These files are backed up on CD and archived.  Copies of CDs can be provided to PIs for display on their computer using the viewing software included on the CD.  Further data analysis can be performed using MATLAB.

Optical:  Currently, each investigator’s images are acquired and saved in a monthly folder.  Images are transferred to an archival storage device (e.g., DVD) on a biweekly basis. The monthly folders can typically be retained on the host computer for 3-4 months before they are deleted.  Images acquired on the Xenogen Ivis® are viewed using the instrument’s Living Image®  software.

Autoradiography:  Images are saved to the investigator’s folder on the host computer.  Once the imaging database system is fully operational, there will be daily backup of acquired images to the CMGI server.  Image files will be routinely archived to a storage device (e.g., DVD).