Additional Resources

 


Software


 

FastSPECT II is a SPECT imaging system developed at CGRI for small-animal imaging. It consists of sixteen stationary (i.e., non-moving) modular gamma-ray cameras. Each camera has an input face measuring about 120×120 mm^2.  GPU code was developed to speed up the pre-processing of the acquired data and the actual reconstruction via the expectation maximization maximum likelihood (MLEM) algorithm. Pre-processing of the data consisted in 2D maximum likelihood estimation of position of interaction for each detected gamma-ray photon.

The one-page highlight can be download here.

The manual for this toolkit can be downloaded here.

For further details and to obtain the FastSPECT II Image Reconstruction Toolbox, please contact Luca Caucci at caucci@email.arizona.edu.

REFERENCES

FastSPECT II: A Second Generation High-Resolution Dynamic SPECT Imager, Lars R. Furenlid, Donald W Wilson, Yi-chun Chen, Hyunki Kim, Philip J. Pietraski, Michael J. Crawford, Harrison H. Barrett, IEEE Trans Nucl Science, 51(3): 631-635, 2004.

Maximum-likelihood estimation with a contracting-grid search algorithm, J. Y. Hesterman, L. Caucci, M. A. Kupinski, H. H. Barrett, and L. R. Furenlid, IEEE Trans. Nucl. Sci., 57(3):1077-1084, 2010.  PMC293245.

Download Toolbox

File size : 8K
To uncompress type:
gunzip ImageQuality.tar.gz
tar xf ImageQuality.tar

INFORMATION

Version 0.9b Mar-25-2001© The University of Arizona
The following is a list of routines available from this toolbox. Detailed information about each routine is available by typing ‘help “fncname”‘ in Matlab.

BACKGROUND GENERATION

LumpyBgnd – Generate a lumpy background — type 1
MVNLumpy – Generate a lumpy background — type 2
MVNLumpyConv- Same as above but without the wrap around artifacts
CLB – Generate a clustered-lumpy background as described by Bochud, et. al. NOTE: CLB and LumpyBgnd require that poissrnd from the Stats toolbox is available.

SIGNAL GENERATION

CircSignal – Generate a circular disc signal
GaussianSignal – Generate a gaussian blob signal

OBSERVERS

Laguerre2D – Generate Laguerre-Gauss functions for approximating the ideal observer
ApplyTemplates – Apply templates to images
CHotelling – Compute the channelized Hotelling observer outputs
Two-alternative-forced choice
Test2AFC – Perform a 2AFC experiment

ROC

WilcoxonAUC – Compute the Wilcoxon area under the ROC curve. This also returns ROC operating points for graphing dprime – Compute the d’ SNR statistic
AzFromDP – Compute the Az from the d’ statisticMiscellaneous
RunExperiment – demonstration of some of these routines — try this

This toolbox is a work in progress. Please report any bugs or suggestions to Matthew Kupinski.

Download Toolbox

File size : 3K
To uncompress type:
gunzip NoGoldEst.tar.gz
tar xf NoGoldEst.tar

INFORMATION

For package information see the files Contents.m and Example.m on how to compare estimation tasks without a gold standard. For information about our method, consult our papers:

This is an implementation of the OneShot algorithm for estimating the dependent of the variance of the area under the ROC curve on the numbers of signal-present cases, signal-absent cases, and readers. This code was designed to be very efficient and to work with large datasets like the ones we generate in our simulations. It works with continuous or categorical data.

Download Toolbox

File size : 24K
To uncompress type:
gunzip OneShot.tar.gz
tar xf OneShot.tar

See ReadMe.txt and source code for more information.

REFERENCES

“A Probabilistic Development of the MRMC Method,” Eric Clarkson, Matthew A. Kupinski, Harrison H. Barrett, Acad Radiol. 13(11):1410-21, 2006

One-Shot Estimate of MRMC Variance: AUC,” Brandon D. Gallas, Academic Radiology 13:353-362, 2006.

This toolkit contains code to perform a variety of image processing procedures on data acquired via the the University of Arizona’s ModCam Labview package. The toolkit handles image processing for list-mode calibration (mean detector response function and point spread function data, including interpolation) and projection data. Code is included to perform reconstructions with ordered-subset expectation maximization (OSEM), including center-of-rotation correction.

The manual for this toolkit can be downloaded here.

Download Toolkit

File size : 76K
To uncompress type:
gunzip ImageProcessingLib.tgz
tar xf ImageProcessingLib.tar

References:
The multi-module, multi-resolution system – A novel small-animal SPECT system,” Jacob Y. Hesterman, Matthew A. Kupinski, Lars Furenlid, Donald W. Wilson, and Harrison H. Barrett, Med Phys. 2007 Mar; 34(3): 987–993.


Literature


A list of CAPP-related papers and other publications can be found at the CAPP publication list at the PubMed site.  Books and book chapters published by CAPP members can be found on our training website.

 


CAPP Resources


 

  • FastSPECT II – a 16-camera preclinical SPECT imager
  • FastSPECT III – dedicated rodent brain imager with iQID detectors and massive GPU support

    FASTSPECTS.png

    Left: the FastSPECT II 16-camera preclinical stationary SPECT imager in the 035 TBIR lab. Right: the FastSPECT III 20-iQID camera rodent-brain imager and frame-parsing computing rack in CAPP laboratory 090J.
  • AdaptiSPECT – an adaptive preclinical SPECT system
  • FaCT – Adaptive preclinical CT system, can be used in tandem with FastSPECT II or AdaptiSPECT
  • SmartCAM – prototype clinical adaptive SPECT system based on a commercial gamma camera
  • ModPET - Low-cost, high-performance preclinical PET imager based on modular cameras and real-time ML event estimation
  • 2-axis, 3-axis, and 5-axis stage systems to accurately position collimated and/or point sources
  • a wide variety of collimators to create low-divergence gamma-ray beams, including from 511 keV
    • traveling equipment for detector characterization at synchrotron light sources
    • shielded concentrating station for calibration source preparation
  • scintillator-radiance-measurement station

•       A high-performance digital radiography and scintigraphy system based on the iQID camera.

•       Fuji BAS 500 autoradiography system -  post-mortem tissue sample images

•       Cryotome for autoradiography

•       Faxitron specimen x-ray system

•       Well counters for biodistribution studies

•       Reconstruction and display workstations

•       Radiotracer delivery, animal injection, hot-animal storage services

•       Labeling reactions with commercial kits

•       Animal prep/anesthesia/acquisition support for the above systems

  • Metcal surface-mount soldering and desoldering equipment (Metcal)
  • APS (Automated Production Systems, Inc) Screen printer for solder-paste deposition
    • APS Gold Place semi-automated pick-and-place machine for board stuffing
    • APS Gold-Flow GF-12 conveyor-belt reflow oven for pick-and-place part soldering
  • Metcal BGA and large IC rework station
  • Branson Ultrasound bath for board cleaning
  • Olympus stereo microscope for small-IC-package solder/desoldering
  • Workstations and licenses for circuit simulation (MultiSIM), design (UltiBoard), and firmware development (MentorGraphics) 
  • Electronics testing hardware including signal generators, power supplies and multiple high-speed digital scopes (Tektronix  DPO 72004B 20GHz, 50 GS/S; Lecroy Wavesurfer 452 500MHz; Tektronix TDS 3034 300 MHz)
  • NIM and VME crates for testing with commercial electronics modules, wide variety of amplifiers, single channel analyzers, and related
  • Wafer prober for electronic testing of custom ASICs prior to wafer dicing
  • Active probes for signal testing on ASICs
  • Site licenses for a variety of design tools, including SolidWorks and AutoCAD
    • Rapid prototype printers for fabrication of metal and plastic parts, engineering models, metal casting molds
  • Wide range of portable fabrication tools, including electro-magnetic drill press, saws, sanders, and lifts
    • Measurement tools including large digital calipers (24”), run-out gauges, laser alignment aids
  • Mechanical shop including digital read-out mill, lathe, band saw, drill press, and stationary sander
  • Sheet-metal cutting, bending, and rolling machine
  • Spot welder and standard tools for plumbing, electrical, and mechanical assembly

Metal.png

The ExOne Innovent metal printer in 090M. This tungsten-powder capable system jets a binder into a powder stock that is cured in an oven and then sintered in a furnace to produce a final metal product.

Plastic.png

Left: CAPP’s Objet Connex 350 Rapid Prototype Printer in laboratory 090M. Right: close up photograph of the build field showing the printing of molds for fabrication of collimator with tungsten-epoxy composite casting.

Custom benchtop multi-spectral confocal microendoscope

•      Mobile clinical confocal microendoscope

•      Nikon C1 confocal on E600 fluorescence microscope

•      LaVision Biotec custom configured intravital microscope with fluorescence, confocal and multi-photon capability. It is equipped with a Ti-Sapphire laser covering the range from 680-1060 nm and has a high sensitivity port that collects non-descanned light for 2P or SHG. (BSRL - TBIR)

  • Large inventory of specialized optical components, optical breadboards, optical tables, and mounting hardware

•      Custom bioluminescence/fluorescence imaging system - The AZ Box – (BSRL-TBIR)

•      Spectral Instruments Lago-X bioluminescence and projection X-ray system (BSRL-TBIR/CISR)

•      Bruker 7.0T Biospec 20cm-bore multi-nuclear NMR/MRI instrument (BSRL – TBIR)

  • Mobile Cart for in vivo Acoustoelectric Brain Imaging (ABI) and AEI in animals.
  • Separate bench-top AEI system in CAPP lab 090E.
  • Broadband microwave pulsers: Epsco PG5KB (<100 nsec pulses, 4kW, 2.7-3.1GHz, 4+kHz PRR)

  •  High power pulsed microwave transmitter (partnered with Dr. Hao Xin) (1.2-1.4 GHz, 25 kW, <10 µs)

  • One Green-pumped Continuum pulsed laser (Surelite-II/20+OPO, tunable 680-2000nm)

  • One Blue-Pumped Continuum pulsed laser (Surelite-II/20+OPO, tunable 410-2000nm)

  • Ocean Optics Photo Spectrometer

  • Home-built ultrasound and photoacoustic microscope imaging system

  • Various MHz and GHz HP signal generators, kV pulsers

  • High power pulsers (~100 MHz)

  • Various microwave waveguides and TEMs for microwave induced thermal imaging and TAI

  • Fast Random Access Camera (1280HF, Silicon Imaging, Inc) to examine radiation force, microbubbles, and laser induced fluorescence

  • Kirlian Photography System

  • Two 16-channel National Instruments Card (PXI 6289) to capture physiological signals (EEG, ECG)
  • Two 16-channel National Instruments Card (PXI-5105) to capture high frequency RF signals (AE, US)
  • 12-Channel Biopac electrical recording system (EEG, EMG, ECG), pulse oximetry, and accessories
  • 8 channels of fast acquisition boards with bandwidth >50 MHz (Signatec)
  • 2-Channel 500 MHz portable digital oscilloscopes (Picoscope 5203)
  • Two Quantum Composer Multichannel Trigger controllers
  • 350 MHz and 500 MHz Lecroy Oscilloscopes (Waverunner 64Xi)
  • Eight high-end PCs for hardware control, data acquisition, analysis, and simulation
  • One BiometricsLDT 4 channel wireless data acquisition system for biosensing (EMG, force, etc.)
  • Seven F Biosense clinical cardiac catheters with multielectrodes
  • Force transducers, dynamometer, Biopac MP150 (for multichannel acquisition of EEG, EMG, force)
  • 11 motorized translation stages (Velmex) for precise positioning tissue, transducers and electrodes
  • Thermocouples for thermometry
  • Custom 16-channel signal conditioning box to collect AE and physiologic signals (EEG, ECG, EMG)
  • 500 MHz ENI power amplifier
  • T&C AG1021 20 MHZ High Power RF Amplifier
  • Biopac STIMSOL electrical stimulator (used in ABI for isolating current in head phantom)
  • Grass Instrument current and voltage stimulators (S88) and isolators
  • Seven high frequency MHz differential amplifiers (Lecroy DA1855A, DA1855A/PR2)