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Article ; Online: In-vivo fluorescence imaging with a multivariate curve resolution spectral unmixing technique.

Xu, Heng / Rice, Brad W

2009 Volume 14, Issue 6, Page(s) 64011

Abstract: Spectral unmixing is a useful technique in fluorescence imaging for reducing the effects of native tissue autofluorescence and separating multiple fluorescence probes. While spectral unmixing methods are well established in fluorescence microscopy, they ... ...

Abstract	Spectral unmixing is a useful technique in fluorescence imaging for reducing the effects of native tissue autofluorescence and separating multiple fluorescence probes. While spectral unmixing methods are well established in fluorescence microscopy, they typically rely on precharacterized in-vitro spectra for each fluorophore. However, there are unique challenges for in-vivo applications, since the tissue absorption and scattering can have a significant impact on the measured spectrum of the fluorophore, and therefore make the in-vivo spectra substantially different to that of in vitro. In this work, we introduce a spectral unmixing algorithm tailored for in-vivo optical imaging that does not rely on precharacterized spectral libraries. It is derived from a multivariate curve resolution (MCR) method, which has been widely used in studies of chemometrics and gene expression. Given multispectral images and a few straightforward constraints such as non-negativity, the algorithm automatically finds the signal distribution and the pure spectrum of each component. Signal distribution maps help separate autofluorescence from other probes in the raw images and hence provide better quantification and localization for each probe. The algorithm is demonstrated with an extensive set of in-vivo experiments using near-infrared dyes and quantum dots in both epi-illumination and transillumination geometries.
MeSH term(s)	Algorithms ; Animals ; Fluorescent Dyes/chemistry ; Least-Squares Analysis ; Mice ; Mice, Nude ; Multivariate Analysis ; Phantoms, Imaging ; Spectrometry, Fluorescence/methods
Chemical Substances	Fluorescent Dyes
Language	English
Publishing date	2009-12-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	1309154-2
ISSN	1560-2281 ; 1083-3668
ISSN (online)	1560-2281
ISSN	1083-3668
DOI	10.1117/1.3258838
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Article ; Online: Adaptive row-action inverse solver for fast noise-robust three-dimensional reconstructions in bioluminescence tomography: theory and dual-modality optical/computed tomography in vivo studies.

Behrooz, Ali / Kuo, Chaincy / Xu, Heng / Rice, Brad

Journal of biomedical optics

2013 Volume 18, Issue 7, Page(s) 76010

Abstract: A novel approach is presented for obtaining fast robust three-dimensional (3-D) reconstructions of bioluminescent reporters buried deep inside animal subjects from multispectral images of surface bioluminescent photon densities. The proposed method ... ...

Abstract	A novel approach is presented for obtaining fast robust three-dimensional (3-D) reconstructions of bioluminescent reporters buried deep inside animal subjects from multispectral images of surface bioluminescent photon densities. The proposed method iteratively acts upon the equations relating the multispectral data to the luminescent distribution with high computational efficiency to provide robust 3-D reconstructions. Unlike existing algebraic reconstruction techniques, the proposed method is designed to use adaptive projections that iteratively guide the updates to the solution with improved speed and robustness. Contrary to least-squares reconstruction methods, the proposed technique does not require parameter selection or optimization for optimal performance. Additionally, optimized schemes for thresholding, sampling, and ordering of the bioluminescence tomographic data used by the proposed method are presented. The performance of the proposed approach in reconstructing the shape, volume, flux, and depth of luminescent inclusions is evaluated in a multitude of phantom-based and dual-modality in vivo studies in which calibrated sources are implanted in animal subjects and imaged in a dual-modality optical/computed tomography platform. Statistical analysis of the errors in the depth and flux of the reconstructed inclusions and the convergence time of the proposed method is used to demonstrate its unbiased performance, low error variance, and computational efficiency.
MeSH term(s)	Algorithms ; Animals ; Imaging, Three-Dimensional/methods ; Implants, Experimental ; Mice ; Mice, Nude ; Models, Theoretical ; Molecular Imaging/methods ; Phantoms, Imaging ; Tomography, Optical/methods ; Tomography, X-Ray Computed
Language	English
Publishing date	2013-05-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	1309154-2
ISSN	1560-2281 ; 1083-3668
ISSN (online)	1560-2281
ISSN	1083-3668
DOI	10.1117/1.JBO.18.7.076010
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Article: Quantitative comparison of the sensitivity of detection of fluorescent and bioluminescent reporters in animal models.

Troy, Tamara / Jekic-McMullen, Dragana / Sambucetti, Lidia / Rice, Brad

Molecular imaging

2004 Volume 3, Issue 1, Page(s) 9–23

Abstract: Bioluminescent and fluorescent reporters are finding increased use in optical molecular imaging in small animals. In the work presented here, issues related to the sensitivity of in vivo detection are examined for standard reporters. A high-sensitivity ... ...

Abstract	Bioluminescent and fluorescent reporters are finding increased use in optical molecular imaging in small animals. In the work presented here, issues related to the sensitivity of in vivo detection are examined for standard reporters. A high-sensitivity imaging system that can detect steady-state emission from both bioluminescent and fluorescent reporters is described. The instrument is absolutely calibrated so that animal images can be analyzed in physical units of radiance allowing more quantitative comparisons to be performed. Background emission from mouse tissue, called autoluminescence and autofluorescence, is measured and found to be an important limitation to detection sensitivity of reporters. Measurements of dual-labeled (bioluminescent/fluorescent) reporter systems, including PC-3M-luc/DsRed2-1 and HeLa-luc/PKH26, are shown. The results indicate that although fluorescent signals are generally brighter than bioluminescent signals, the very low autoluminescent levels usually results in superior signal to background ratios for bioluminescent imaging, particularly compared with fluorescent imaging in the green to red part of the spectrum. Fluorescence detection sensitivity improves in the far-red to near-infrared, provided the animals are fed a low-chlorophyll diet to reduce autofluorescence in the intestinal region. The use of blue-shifted excitation filters is explored as a method to subtract out tissue autofluorescence and improve the sensitivity of fluorescent imaging.
MeSH term(s)	Adenocarcinoma/metabolism ; Adenocarcinoma/pathology ; Animals ; Cell Line, Tumor ; Diagnostic Imaging/instrumentation ; Diagnostic Imaging/methods ; Female ; Fluorescence ; Fluorescent Dyes/metabolism ; HeLa Cells ; Humans ; Luminescent Measurements ; Luminescent Proteins/analysis ; Luminescent Proteins/metabolism ; Male ; Mice ; Mice, Inbred Strains ; Mice, Nude ; Models, Animal ; Optics and Photonics ; Organic Chemicals/metabolism ; Prostatic Neoplasms/metabolism ; Prostatic Neoplasms/pathology ; Sensitivity and Specificity
Chemical Substances	Fluorescent Dyes ; Luminescent Proteins ; Organic Chemicals ; PKH 26 ; fluorescent protein 583
Language	English
Publishing date	2004-01
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	2137435-1
ISSN	1536-0121 ; 1535-3508
ISSN (online)	1536-0121
ISSN	1535-3508
DOI	10.1162/15353500200403196
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Article ; Online: Multispectral Cerenkov luminescence tomography for small animal optical imaging.

Spinelli, Antonello E / Kuo, Chaincy / Rice, Brad W / Calandrino, Riccardo / Marzola, Pasquina / Sbarbati, Andrea / Boschi, Federico

Optics express

2011 Volume 19, Issue 13, Page(s) 12605–12618

Abstract: Quite recently Cerenkov luminescence imaging (CLI) has been introduced as a novel pre-clinical imaging for the in vivo imaging of small animals such as mice. The CLI method is based on the detection of Cerenkov radiation (CR) generated by beta particles ... ...

Abstract	Quite recently Cerenkov luminescence imaging (CLI) has been introduced as a novel pre-clinical imaging for the in vivo imaging of small animals such as mice. The CLI method is based on the detection of Cerenkov radiation (CR) generated by beta particles as they travel into the animal tissues with an energy such that Cerenkov emission condition is satisfied. This paper describes an image reconstruction method called multi spectral diffuse Cerenkov luminescence tomography (msCLT) in order to obtain 3D images from the detection of CR. The multispectral approach is based on a set of 2D planar images acquired using a number of narrow bandpass filters, and the distinctive information content at each wavelength is used in the 3D image reconstruction process. The proposed msCLT method was tested both in vitro and in vivo using 32P-ATP and all the images were acquired by using the IVIS 200 small animal optical imager (Caliper Life Sciences, Alameda USA). Source depth estimation and spatial resolution measurements were performed using a small capillary source placed between several slices of chicken breast. The theoretical Cerenkov emission spectrum and optical properties of chicken breast were used in the modelling of photon propagation. In vivo imaging was performed by injecting control nude mice with 10 MBq of 32P-ATP and the 3D tracer bio-distribution was reconstructed. Whole body MRI was acquired to provide an anatomical localization of the Cerenkov emission. The spatial resolution obtained from the msCLT reconstructed images of the capillary source showed that the FWHM is about 1.5 mm for a 6 mm depth. Co-registered MRI images showed that the Cerenkov emission regions matches fairly well with anatomical regions, such as the brain, heart and abdomen. Ex vivo imaging of the different organs such as intestine, brain, heart and ribs further confirms these findings. We conclude that in vivo 3D bio-distribution of a pure beta-minus emitting radiopharmaceutical such as 32P-ATP can be obtained using the msCLT reconstruction approach.
MeSH term(s)	Adenosine Triphosphate/pharmacokinetics ; Algorithms ; Animals ; Beta Particles ; Capillaries ; Chickens ; Computer Simulation ; Electrons ; Image Processing, Computer-Assisted/instrumentation ; Image Processing, Computer-Assisted/methods ; Luminescence ; Magnetic Resonance Imaging ; Mice ; Mice, Nude ; Models, Theoretical ; Muscle, Skeletal/blood supply ; Muscle, Skeletal/diagnostic imaging ; Phantoms, Imaging ; Phosphorus Radioisotopes ; Positron-Emission Tomography/instrumentation ; Positron-Emission Tomography/methods ; Tissue Distribution
Chemical Substances	Phosphorus Radioisotopes ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2011-06-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.19.012605
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Preclinical Validation of the Utility of BLZ-100 in Providing Fluorescence Contrast for Imaging Spontaneous Solid Tumors.

Fidel, Janean / Kennedy, Katie C / Dernell, William S / Hansen, Stacey / Wiss, Valorie / Stroud, Mark R / Molho, Joshua I / Knoblaugh, Sue E / Meganck, Jeffrey / Olson, James M / Rice, Brad / Parrish-Novak, Julia

Cancer research

2014 Volume 75, Issue 20, Page(s) 4283–4291

Abstract: There is a need in surgical oncology for contrast agents that can enable real-time intraoperative visualization of solid tumors that can enable complete resections while sparing normal surrounding tissues. The Tumor Paint agent BLZ-100 is a peptide- ... ...

Abstract	There is a need in surgical oncology for contrast agents that can enable real-time intraoperative visualization of solid tumors that can enable complete resections while sparing normal surrounding tissues. The Tumor Paint agent BLZ-100 is a peptide-fluorophore conjugate that can specifically bind solid tumors and fluoresce in the near-infrared range, minimizing light scatter and signal attenuation. In this study, we provide a preclinical proof of concept for use of this imaging contrast agent as administered before surgery to dogs with a variety of naturally occurring spontaneous tumors. Imaging was performed on excised tissues as well as intraoperatively in a subset of cases. Actionable contrast was achieved between tumor tissue and surrounding normal tissues in adenocarcinomas, squamous cell carcinomas, mast cell tumors, and soft tissue sarcomas. Subcutaneous soft tissue sarcomas were labeled with the highest fluorescence intensity and greatest tumor-to-background signal ratio. Our results establish a foundation that rationalizes clinical studies in humans with soft tissue sarcoma, an indication with a notably high unmet need.
MeSH term(s)	Adolescent ; Animals ; Child ; Child, Preschool ; Contrast Media/administration & dosage ; Diagnostic Imaging/instrumentation ; Diagnostic Imaging/methods ; Disease Models, Animal ; Dogs ; Female ; Fluorescent Dyes/administration & dosage ; Humans ; Indocyanine Green/administration & dosage ; Indocyanine Green/analogs & derivatives ; Intraoperative Care ; Male ; Neoplasms/diagnosis ; Neoplasms/pathology ; Reproducibility of Results ; Scorpion Venoms/administration & dosage
Chemical Substances	Contrast Media ; Fluorescent Dyes ; Scorpion Venoms ; tozuleristide (835UH424TU) ; Indocyanine Green (IX6J1063HV)
Language	English
Publishing date	2014-08-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1432-1
ISSN	1538-7445 ; 0008-5472
ISSN (online)	1538-7445
ISSN	0008-5472
DOI	10.1158/0008-5472.CAN-15-0471
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Article: Three-dimensional reconstruction of in vivo bioluminescent sources based on multispectral imaging.

Kuo, Chaincy / Coquoz, Olivier / Troy, Tamara L / Xu, Heng / Rice, Brad W

Journal of biomedical optics

2006 Volume 12, Issue 2, Page(s) 24007

Abstract: A new method is described for obtaining a 3-D reconstruction of a bioluminescent light source distribution inside a living animal subject, from multispectral images of the surface light emission acquired on charge-coupled device (CCD) camera. The method ... ...

Abstract	A new method is described for obtaining a 3-D reconstruction of a bioluminescent light source distribution inside a living animal subject, from multispectral images of the surface light emission acquired on charge-coupled device (CCD) camera. The method uses the 3-D surface topography of the animal, which is obtained from a structured light illumination technique. The forward model of photon transport is based on the diffusion approximation in homogeneous tissue with a local planar boundary approximation for each mesh element, allowing rapid calculation of the forward Green's function kernel. Absorption and scattering properties of tissue are measured a priori as input to the algorithm. By using multispectral images, 3-D reconstructions of luminescent sources can be derived from images acquired from only a single view. As a demonstration, the reconstruction technique is applied to determine the location and brightness of a source embedded in a homogeneous phantom subject in the shape of a mouse. The technique is then evaluated with real mouse models in which calibrated sources are implanted at known locations within living tissue. Finally, reconstructions are demonstrated in a PC3M-luc (prostate tumor line) metastatic tumor model in nude mice.
MeSH term(s)	Animals ; Image Interpretation, Computer-Assisted/methods ; Imaging, Three-Dimensional/methods ; Luminescent Proteins/analysis ; Male ; Mice ; Microscopy, Fluorescence, Multiphoton/methods ; Prostatic Neoplasms/pathology ; Whole Body Imaging/methods
Chemical Substances	Luminescent Proteins
Language	English
Publishing date	2006-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1309154-2
ISSN	1083-3668
ISSN	1083-3668
DOI	10.1117/1.2717898
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Article ; Online: Monitoring bacterial burden, inflammation and bone damage longitudinally using optical and μCT imaging in an orthopaedic implant infection in mice.

Niska, Jared A / Meganck, Jeffrey A / Pribaz, Jonathan R / Shahbazian, Jonathan H / Lim, Ed / Zhang, Ning / Rice, Brad W / Akin, Ali / Ramos, Romela Irene / Bernthal, Nicholas M / Francis, Kevin P / Miller, Lloyd S

PloS one

2012 Volume 7, Issue 10, Page(s) e47397

Abstract: Background: Recent advances in non-invasive optical, radiographic and μCT imaging provide an opportunity to monitor biological processes longitudinally in an anatomical context. One particularly relevant application for combining these modalities is to ... ...

Abstract	Background: Recent advances in non-invasive optical, radiographic and μCT imaging provide an opportunity to monitor biological processes longitudinally in an anatomical context. One particularly relevant application for combining these modalities is to study orthopaedic implant infections. These infections are characterized by the formation of persistent bacterial biofilms on the implanted materials, causing inflammation, periprosthetic osteolysis, osteomyelitis, and bone damage, resulting in implant loosening and failure. Methodology/principal findings: An orthopaedic implant infection model was used in which a titanium Kirshner-wire was surgically placed in femurs of LysEGFP mice, which possess EGFP-fluorescent neutrophils, and a bioluminescent S. aureus strain (Xen29; 1×10(3) CFUs) was inoculated in the knee joint before closure. In vivo bioluminescent, fluorescent, X-ray and μCT imaging were performed on various postoperative days. The bacterial bioluminescent signals of the S. aureus-infected mice peaked on day 19, before decreasing to a basal level of light, which remained measurable for the entire 48 day experiment. Neutrophil EGFP-fluorescent signals of the S. aureus-infected mice were statistically greater than uninfected mice on days 2 and 5, but afterwards the signals for both groups approached background levels of detection. To visualize the three-dimensional location of the bacterial infection and neutrophil infiltration, a diffuse optical tomography reconstruction algorithm was used to co-register the bioluminescent and fluorescent signals with μCT images. To quantify the anatomical bone changes on the μCT images, the outer bone volume of the distal femurs were measured using a semi-automated contour based segmentation process. The outer bone volume increased through day 48, indicating that bone damage continued during the implant infection. Conclusions/significance: Bioluminescent and fluorescent optical imaging was combined with X-ray and μCT imaging to provide noninvasive and longitudinal measurements of the dynamic changes in bacterial burden, neutrophil recruitment and bone damage in a mouse orthopaedic implant infection model.
MeSH term(s)	Animals ; Bacterial Load ; Bone and Bones/diagnostic imaging ; Bone and Bones/pathology ; Fluorescence ; Implants, Experimental/adverse effects ; Inflammation/complications ; Inflammation/diagnostic imaging ; Inflammation/pathology ; Knee Joint/diagnostic imaging ; Knee Joint/microbiology ; Knee Joint/pathology ; Knee Joint/surgery ; Male ; Mice ; Neutrophil Infiltration ; Optical Imaging ; Orthopedics ; Prosthesis-Related Infections/complications ; Prosthesis-Related Infections/diagnostic imaging ; Prosthesis-Related Infections/microbiology ; Prosthesis-Related Infections/pathology ; Staphylococcus aureus/growth & development ; X-Ray Microtomography
Language	English
Publishing date	2012-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0047397
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Article: Reduction of Astrogliosis by Early Treatment of Pneumococcal Meningitis Measured by Simultaneous Imaging, In Vivo, of the Pathogen and Host Response

Kadurugamuwa, Jagath L / Modi, Kshitij / Coquoz, Olivier / Rice, Brad / Smith, Steven / Contag, Pamela R / Purchio, Tony

Infection and immunity. 2005 Dec., v. 73, no. 12

2005

Abstract: We developed a method for simultaneous in vivo biophotonic monitoring of pneumococcal meningitis and the accompanying neuronal injury in live transgenic mice. Streptococcus pneumoniae engineered for bioluminescence (lux) was used for direct visualization ...

Abstract	We developed a method for simultaneous in vivo biophotonic monitoring of pneumococcal meningitis and the accompanying neuronal injury in live transgenic mice. Streptococcus pneumoniae engineered for bioluminescence (lux) was used for direct visualization of disease progression and antibiotic treatment in a mouse model of meningitis. The host response was monitored in transgenic mice containing an inducible firefly luciferase (luc) reporter gene under transcriptional control of the mouse glial fibrillary acidic protein (GFAP) promoter. Based on the different spectra of light emission and substrate requirements for lux and luc, we were able to separately monitor the two reporters using a highly sensitive in vivo imaging system. The level of neuronal damage and recovery following antibiotic treatment was dependent on the time of treatment. This model has potential for simultaneous multiparameter monitoring and testing of therapies that target the pathogen or host response to prevent neuronal injury and recovery.
Keywords	Streptococcus pneumoniae ; animal models ; antibiotics ; bioluminescence ; disease course ; image analysis ; luciferase ; meningitis ; mice ; monitoring ; pathogens ; reporter genes ; transcription (genetics)
Language	English
Size	p. 7836-7843.
Publishing place	American Society for Microbiology
Document type	Article
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
Database	NAL-Catalogue (AGRICOLA)

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Article: Reduction of astrogliosis by early treatment of pneumococcal meningitis measured by simultaneous imaging, in vivo, of the pathogen and host response.

Kadurugamuwa, Jagath L / Modi, Kshitij / Coquoz, Olivier / Rice, Brad / Smith, Steven / Contag, Pamela R / Purchio, Tony

Infection and immunity

2005 Volume 73, Issue 12, Page(s) 7836–7843

Abstract	We developed a method for simultaneous in vivo biophotonic monitoring of pneumococcal meningitis and the accompanying neuronal injury in live transgenic mice. Streptococcus pneumoniae engineered for bioluminescence (lux) was used for direct visualization of disease progression and antibiotic treatment in a mouse model of meningitis. The host response was monitored in transgenic mice containing an inducible firefly luciferase (luc) reporter gene under transcriptional control of the mouse glial fibrillary acidic protein (GFAP) promoter. Based on the different spectra of light emission and substrate requirements for lux and luc, we were able to separately monitor the two reporters using a highly sensitive in vivo imaging system. The level of neuronal damage and recovery following antibiotic treatment was dependent on the time of treatment. This model has potential for simultaneous multiparameter monitoring and testing of therapies that target the pathogen or host response to prevent neuronal injury and recovery.
MeSH term(s)	Animals ; Anti-Bacterial Agents/therapeutic use ; Astrocytes/pathology ; Brain/microbiology ; Brain/pathology ; Disease Models, Animal ; Genes, Reporter ; Glial Fibrillary Acidic Protein/genetics ; Gliosis/drug therapy ; Gliosis/pathology ; Luciferases, Firefly/analysis ; Luciferases, Firefly/genetics ; Luminescent Agents/analysis ; Luminescent Measurements ; Meningitis, Pneumococcal/drug therapy ; Meningitis, Pneumococcal/microbiology ; Meningitis, Pneumococcal/pathology ; Mice ; Mice, Transgenic ; Promoter Regions, Genetic/genetics ; Streptococcus pneumoniae/genetics
Chemical Substances	Anti-Bacterial Agents ; Glial Fibrillary Acidic Protein ; Luminescent Agents ; Luciferases, Firefly (EC 1.13.12.7)
Language	English
Publishing date	2005-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
DOI	10.1128/IAI.73.12.7836-7843.2005
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