After adeno-Cre instillation, tumors were monitored via MRI and when tumor burden was measurable, mice were placed on one of four arms of a treatment regimen. Animals were anaesthetized via inhalation of isoflurane and kept warm on heated waterbed, vitals were monitored via cardiac and respiratory cycle (SA instruments), and recorded every 10 minutes while the animal was under anesthesia. The SA instruments pneumatic respiratory monitor was used to remove breathing artifacts by gating on the respiratory cycle. The Bruker ClinScan system used to scan the animals had 12 cm of actively shielded gradients, maximum strength 630 mT/m, and a slew rate of 6,300 T/m/second. This instrument is a 7T system with 2 × 2 array coil and 2D gradient echoT1-weighted sequences. The parameters used for imaging are as follows: 18 slices, TR = 170 ms, TE = 2.4 ms, α = 38°, Navg = 3, FOV 26 × 26 mm2, 1 mm thickness, matrix size 256 × 256, for a voxel size of 0.102 × 0.102 × 1.0 mm. In 2021, the system was upgraded to a Bruker Biospec system. For this upgraded machine, the Bruker IntraGate software was used to remove respiratory and cardiac motion with parameters: 18 slices, TR = 8.96ms ms, TE = 3.4 ms, α = 10°, oversampling = 28, FOV 26 × 26 mm2, 1 mm thickness, matrix size 192 × 192, 10 minutes. Models were then built on Slicer three-dimensional (3D) software to calculate tumor volume.
Intragate software
Manufactured by Bruker
IntraGate software is a tool developed by Bruker for the analysis of ECG-gated cardiac images. It provides functionality for the visualization and processing of cardiac data obtained from various imaging modalities.
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5 protocols using intragate software
1
Quantifying Tumor Burden via 7T MRI
2
Cardiac Function Assessment in Mice
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Mice were anesthetized with isoflurane (2%) and imaged in a vertical 9.4-T, 89-mm bore size magnet equipped with 1500 mT/m gradients and connected to an advanced 400 MR system (Bruker Biospin) using a quadrature-driven birdcage coil with an inner diameter of 3 cm. Respiration and ECG were continuously monitored and maintained at 20–60 breaths per minute and 400–600 bpm, respectively. ParaVison 4.0 and IntraGate software (Bruker Biospin GmH) were used for cine MR acquisition and reconstruction. After orthogonal scout imaging, short-axis (oriented perpendicular to the septum) cardiac cine MR images were acquired. Semi-automatic contour detection software (CVI42 (link), version 5.6.6, Circle Cardiovascular Imaging, Canada) was used for the determination of the LV end-diastolic volume, LV end-systolic volume, stroke volume, and ejection fraction (EF), as described53 (link).
3
Cardiac MRI Measurements in Mice
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Cardiac MRI measurements have been previously described in more detail [12 (link)]. After anesthesia with 2% isoflurane, mice were placed in a vertical 9.4-T, 89-mm bore size magnet equipped with 1500 mT/m gradients and connected to an advanced 400 MR system (Bruker Biospin) using a quadrature-driven birdcage coil with an inner diameter of 3 cm. With the ECG Trigger Unit (RAPID biomedical GmBH), respiration and heart rate were registered. Respiration rate was kept between 20–60 breaths per minute and heart rate between 400–600 beats per minute. Cine MR acquisition and reconstruction was performed with ParaVison 4.0 and IntraGate software (Bruker Biospin GmH). For mice with ischemic heart failure, 8–9 slices were needed for cardiac cine MR images and 7 for control animals. The software QMass (version MR 6.1.5, Medis Medical Imaging Systems) was used to obtain the left ventricular (LV) end-diastolic volume (LVEDV), LV end-systolic volume (LVESV) and LV ejection fraction (LVEF).
4
Tumor Monitoring via MRI and Volumetric Analysis
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After adeno-Cre instillation, tumors were monitored via magnetic resonance imaging (MRI) and when tumor burden was measurable, mice were placed on one of four arms of a treatment regimen. Animals were anaesthetized via inhalation of isoflurane and kept warm on heated waterbed, vitals were monitored via cardiac and respiratory cycle (SA instruments), and recorded every 10 minutes while the animal was under anesthesia. The SA instruments pneumatic respiratory monitor was used to remove breathing artifacts by gating on the respiratory cycle. The Bruker ClinScan system used to scan the animals had 12 cm of actively shielded gradients, maximum strength 630 mT/m, and a slew rate of 6300 T/m/s. This instrument is a 7T system with 2x2 array coil and 2D gradient echoT1-weighted sequences. The parameters used for imaging are as follows: 18 slices, TR = 170 ms, TE = 2.4 ms, α=38°, Navg=3, FOV 26 x 26 mm2 (link), 1mm thickness, matrix size 256 x 256, for a voxel size of 0.102 x 0.102 x 1.0 mm. In 2021, the system was upgraded to a Bruker Biospec system. For this upgraded machine, the Bruker IntraGate software was used to remove respiratory and cardiac motion with parameters: 18 slices, TR = 8.96ms ms, TE = 3.4 ms, α=10°, oversampling = 28, FOV 26 x 26 mm2, 1mm thickness, matrix size 192 x 192, 10 minutes. Models were then built on Slicer 3D software to calculate tumor volume.
5
Cardiac Ventricular Volume Measurement
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Cardiac images were reconstructed using the software tools available in Bruker's Intragate software. Residual navigator pulse trace discontinuities were excluded.
Heart rates for each acquired slice were individually outputted as part of this process. Images were analysed using Image J (Schneider et al., 2012) . Three independent researchers were trained in cardiac image analysis and then each conducted a separate analysis of all images. Researchers were blinded to which subjects the images came from.
For each slice, images were acquired for 10 different phases of the cardiac cycle.
From the 10 images of the cardiac cycle for the central chamber, the images corresponding to the diastolic and systolic phases were identified. For each slice at diastole and systole, a region of interest was manually drawn around the heart perimeter giving the area of the ventricle at diastole and systole. This area is then converted to a volume for that slice by multiplying by the image slice thickness of 1.5mm. The total ventricular volume of the heart, the end diastolic volume (EDV) and end systolic volume (ESV) are then given by summing the volumes from each slice.
The cardiac ejection fraction (EJ) was then determined by,
Heart rates for each acquired slice were individually outputted as part of this process. Images were analysed using Image J (Schneider et al., 2012) . Three independent researchers were trained in cardiac image analysis and then each conducted a separate analysis of all images. Researchers were blinded to which subjects the images came from.
For each slice, images were acquired for 10 different phases of the cardiac cycle.
From the 10 images of the cardiac cycle for the central chamber, the images corresponding to the diastolic and systolic phases were identified. For each slice at diastole and systole, a region of interest was manually drawn around the heart perimeter giving the area of the ventricle at diastole and systole. This area is then converted to a volume for that slice by multiplying by the image slice thickness of 1.5mm. The total ventricular volume of the heart, the end diastolic volume (EDV) and end systolic volume (ESV) are then given by summing the volumes from each slice.
The cardiac ejection fraction (EJ) was then determined by,
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