Resources

Description: The goal of this toolbox is to provide research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on MATLAB code, and includes code for designing radiofrequency (RF) pulses, readout gradients, and data reconstruction. As part of this source code repository you can also become a contributor to project and add any code of your own or fix/improve the current software.

Reference: Larson, P. E. Z. et al. LarsonLab/Hyperpolarized-Mri-Toolbox: V1.2. Zenodo, 2018. DOI: 10.5281/zenodo.1198915

Description: This code can be used in bioreactor kinetic analysis for inputless unidirectional k_PL modeling.

Preclinical Reference: Ahamed F, Van Criekinge M, Wang ZJ, Kurhanewicz J, Larson P, Sriram R. Modeling hyperpolarized lactate signal dynamics in cells, patient-derived tissue slice cultures and murine models. NMR Biomed. 2021 Jan 07; e4467. doi:10.1002/nbm.4467. Publication Link

Clinical Reference: Larson PEZ, Chen HY, Gordon JW, Korn N, Maidens J, Arcak M, Tang S, van Criekinge M, Carvajal L, Mammoli D, Bok R, Aggarwal R, Ferrone M, Slater JB, Nelson SJ, Kurhanewicz J, Vigneron DB. Investigation of analysis methods for hyperpolarized ¹³C-pyruvate metabolic MRI in prostate cancer patients. NMR Biomed. 2018; 31(11): e3997. PMCID: PMC6392436. Publication Link

Description: SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.

Additional useful links for implementing the SIVIC software:

• SIVIC Tutorials and Users Guide
• Download Sample C-13 Data
• Data Analysis Review Article
• SIVIC Source Code
• PyDICOM Tool Box

Description: We have the 2D SPSP EPI sequence available through Github, please email [email protected]

Description: Spectral-Spatial RF Pulse Design for MRI and MRSI MATLAB Package Originally Written by: Adam B. Kerr and Peder E. Z. Larson. This package includes Matlab functions to design spectral-spatial RF pulses (also known as spatial-spectral RF pulses) for application to magnetic resonance spectroscopy and imaging.

This resource is an update to the bbEPI demo notebook and new 7T spectral spatial example.

Design Method References: 

• Kerr, A.B., Larson,P. E., Lustig, M., Cunningham, C. H., Chen, A. P., Vigneron, D. B., and Pauly, J. M. Multiband spectral-spatial design for high-field and hyperpolarized C-13 applications. In Proceedings of the 16th Annual Meeting of ISMRM (Toronto, 2008), p. 226.
• Larson PE, Kerr AB, Chen AP, Lustig MS, Zierhut ML, Hu S, Cunningham CH, Pauly JM, Kurhanewicz J, Vigneron DB. Multiband excitation pulses for hyperpolarized ¹³C dynamic chemical-shift imaging. J Magn Reson. 2008 Sep;194(1):121-7. doi: 10.1016/j.jmr.2008.06.010. PMCID: PMC3739981. Publication Link

Description: This is an example 2D CSI Data Set. For any questions please email [email protected]

Description: This phantom recipe is courtesy of Ralph Hurd (GE Healthcare) and uses single-labeled C-13 Urea (with natural abundance N-14).

Bone Decalcification Protocol: This protocol describes the steps required for successful decalcification.  Decalcification describes the technique for removing minerals from bone or other calcified tissue so that good-quality paraffin sections can be prepared that will preserve all the essential microscopic elements.  Decalcification is carried out after the specimen has been thoroughly fixed and prior to routine processing to paraffin.

Intratibial Implantation of Tumor Cells: This protocol describes the steps required for a successful implantation of small-cell neuroendocrine prostate cancer PDX cells in the bone tibia. Bone is one of the most common sites for development of metastatic prostate cancer and its study is important for evaluating the tumor characteristics and response to therapy.

Intrahepatic Implantation of Tumor Cells: This protocol describes the steps required for a successful implantation of small-cell neuroendocrine prostate cancer PDX cells in the liver. Liver is one of the most common sites for development of metastatic prostate cancer and its study is important for evaluating the tumor characteristics and response to therapy.

Single Cell Digestion of Tumor Tissue: The purpose of this protocol is to provide details on how to obtain a single-cell suspension from a primary human tumor. 

STR profile of Prostate cancer PDX lines: The protocols for the cell lines LTL610, LTL545, LTL352 and LTL331 are available upon request. Please email [email protected] with your name, title, institution information and brief project description.

Sub-renal Capsule (SRC) Implantation of Tumor Tissue: This protocol describes the steps required for successful implantation of tumor sections under the sub renal capsule. The sub-renal capsule is an optimum site for the propagation of tumor tissue as it provides an environment rich with blood vessels and growth factors. 

Total Lactate Dehydrogenase (LDH) Calorimetric Enzyme Activity Measurement: Lactate Dehydrogenase is a key cytoplasmic enzyme that confers the observed Warburg effect in tumors. Its a tetrameric protein composed of combinations of one or two isomers. This protein catalyzes the reversible reaction pyruvate to lactate. This reaction is monitored spectrophotometrically by observing the reduction in absorbance of NADH (which is maximal at 420nm) as pyruvate is converted to lactate. This protocol, details the steps involved in such a calorimetric assay of cells and tissues.

Pyruvate Preparation for Dissolution DNP: This document goes over the Formulation of Carbon-13 Labeled Pyruvate for Dissolution-DNP. The protocol includes the following: Glassing and High Compound Concentration; Trityl Radical Storage, Measuring T₁ and polarization levels in VNMRJ, Quality Assurance (QA) Procedure for HP Formulations using Hypersense

Bruker HP ¹³C 2D CSI Data Processing Pipeline: This document goes over the Bruker SIVIC pipeline for processing 2D CSI data. Topic areas include: processing overview, data acquisition and the data processing pipeline (preparing spectra for SIVIC, denoising, metabolite maps, SNR map, ratio maps and kinetic maps).

2D CSI Binary Files & Reordering Scripts: This folder contains the Centric Encoding and Linear Encoding files for 2D CSI. Please read the "READ ME Processing C-13 2D CSI Data on SIVIC File" in this folder to implement these files and scripts.

STAR Protocols: Metabolic imaging with hyperpolarized [1-¹³C] pyruvate in patient-derived preclinical mouse models of breast cancer: ¹³C nuclear spin hyperpolarization can increase the sensitivity of detection in an MRI experiment by more than 10,000-fold. ¹³C magnetic resonance spectroscopic imaging (MRSI) of hyperpolarized 13C label exchange between injected [1-¹³C]pyruvate and the endogenous tumor lactate pool can be used clinically to assess tumor grade and response to treatment. This externally hosted STAR Protocol lists an an experimental protocol for using this technique in patient-derived and established cell line xenograft models of breast cancer in the mouse. All credts to Ros et.al.  https://doi.org/10.1016/j.xpro.2021.100608