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Analyzepro

Manufactured by AnalyzeDirect
Sourced in United States

AnalyzePro is a versatile and high-performance laboratory equipment designed for a wide range of analytical applications. It features advanced technology, precision, and reliability to support various scientific research and testing needs.

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9 protocols using analyzepro

1

Quantifying Cementum Morphology via μCT

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Hemi-mandibles and limbs were scanned in a µCT 50 scanner (Scanco Medical, Bassersdorf, Switzerland) at 70 kVp, 76 µA, 0.5 Al filter, 900 ms integration time, and 2 or 6 µm voxel dimension. Reconstructed images were calibrated to 5 known densities of hydroxyapatite and analyzed using AnalyzePro (version 1.0; AnalyzeDirect, Overland Park, KS). Cementum was traced as previously described [4 (link)]. In brief, reconstructed images underwent a median filter, 11 kernel size, and a mask of cementum was generated with a density range of 450–1175 mg HA/cm3, this mask was then overlaid onto the original scan and then cementum is defined as mineralized tissue above 650 mg HA/cm3 in masked area. Based on previous histological and microCT analyses of WT mice, the cervical 2/3 of cementum was designated as acellular cementum, and the apical 1/3 was designated as cellular cementum [4 (link)].
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2

Quantifying Dental Tissue Thickness via μCT

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Human teeth were scanned in a µCT 50 scanner (Scanco Medical, Bassersdorf, Switzerland) at 70 kVp, 76 µA, 0.5 Al filter, 900 ms integration time, and 10 µm voxel dimension. Mouse hemi‐mandibles were scanned under the same parameters except for 6 µm voxel dimension. DICOM files were created from raw data, exported, and calibrated to five known densities of hydroxyapatite (mg/cm3 HA), as previously described (Shin, Chavez, Ikeda, Foster, & Bartlett, 2018). Reconstructed images were analyzed using AnalyzePro (version 1.0; AnalyzeDirect, Overland Park, KS). For both human teeth and mouse first mandibular molars, enamel was segmented semi‐automatically (with manual corrections where necessary) at 1,600 mg/cm3 HA, and dentin/cementum was segmented at 650 mg/cm3 HA, as previously described (Shin et al., 2018). Average dentin thickness was determined for regions of interest (ROIs) by adapting algorithms defined for cortical bone analysis (Bouxsein et al., 2010). The crown dentin ROI initiated 60 µm coronal to the CEJ and extended 150 µm coronally, while the root dentin ROI initiated 300 µm apical to the CEJ and extended 150 µm apically. Mouse crown dentin thickness was measured in the 150 µm of dentin coronal to the CEJ, and root dentin thickness was measured in the central 150 µm of the mesial root.
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3

Quantitative Bone Morphology Analysis

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Mouse femurs from different ages of WT, AgerAHA/+, AgerAHA/AHA, Ager+/−, and Ager−/− mice were harvested, fixed for 48 hr in 10% neutral buffered formalin. A quantitative analysis of the gross bone morphology and microarchitecture was performed using ScanCo microCT 100 system (University at Buffalo). 3D reconstruction and bone microarchitecture analysis were performed using AnalyzePro (AnalyzeDirect Inc).
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4

Quantifying Mineralized Tissue Properties

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Hemi-mandibles and forepaws were scanned in a μCT 50 scanner (Scanco Medical, Bassersdorf, Switzerland) at 70 kVp, 76 μA, 0.5 Al filter, 900 ms integration time, and 6 μm (mandible) or 10 μm (forepaw) voxel dimension. Reconstructed images were calibrated to 5 known densities of hydroxyapatite and analyzed using AnalyzePro (version 1.0; AnalyzeDirect, Overland Park, KS). Mineral density heat maps were generated for forepaws and mandibles. A threshold of 650 mg HA/cm3 was set for mineralized tissue of forepaws. Mandible regions of interest were defined from 480 μm forward from the mesial root and 480 μm backward to the distal root, using the most mesial and distal root points as landmarks. For mandibles, thresholds were set for enamel (1650 mg HA/cm3) and dentin/cementum/bone (650 mg HA/cm3) to determine enamel, dentin, and alveolar bone volumes and densities as previously described [24 (link)–26 (link)]. Measurements were performed in combined male and female animals as sex specific analysis did not alter the findings.
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5

Bone Volume and Alveolar Measurements

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Maxillae were fixed and scanned as previously described (37 (link)). The examiners were blinded to the origin of the samples. Three-dimensional images were generated and rotated with a standard orientation. Bone volume fraction was measured as the percentage of bone volume within the total volume (ROI) using AnalyzePro software (AnalyzeDirect, Inc., Overland Park, KS). Additionally, three liner measurements of the distance from the cemento-enamel junction (CEJ) to the alveolar bone crest (ABC) were taken for the first and second molars as described previously (38 (link), 39 (link)).
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6

Cervical Muscle Differences in Chronic Neck Pain

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This cross-sectional observational study compared the muscle volume, relative volume and the percentage of MFI of cervical extensor and flexor muscles (from C3 to T1) between participants with chronic idiopathic neck pain and asymptomatic age and sex-matched controls. Individuals with chronic idiopathic neck pain (> 3 months) were recruited from a regional city in Australia from the local community via advertisement. Each participant attended two data collection sessions, one where they had clinical measurements conducted, including self-report questionnaires and cervical range of motion, and a second session where they had an MRI examination of the cervical spine. Two blinded researchers (SS, HJT) who did not participate in data collection contoured muscle borders in Analyze Pro (Analyze Direct, Inc., Overland Park, KS, USA) to quantify muscle volume and subsequently relative volume and MFI from MRI. This research was performed according to the Declaration of Helsinki and the study was approved by the Human Research Ethics Committee of the University of Newcastle (H-2015-0235). Informed consent was gained prior to data collection.
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7

Quantifying Midline Shift and Stroke Volume

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MLS and stroke volume were previously measured in EPITHET, MR RESCUE and GAMES-RP trials. For the NINDS tPA trial, stroke volumes are available, and MLS was coded as present or absent. In SPOTRIAS, StopStroke and the stroke registry cohorts, MLS was measured on computed tomography or magnetic resonance imaging axial FLAIR sequence by first laying a straight line between the anterior and posterior attachment of the falx cerebri. MLS was quantified by drawing and measuring a second, perpendicular line to the septum pellucidum at the point of maximal deviation from the midline. Stroke volume was measured on diffusion-weighted MRI or follow-up computed tomography using a semi-automated seed-based method (AnalyzePro, Analyze Direct, Minneapolis, MN). Image analysis was performed while blinded to outcome data. When multiple scans were available, we recorded MLS from the scan (either MRI or CT) with the greatest degree of shift. Details on timing of scans used for volume and MLS measurement are available in Supplementary Table 1. We divided those patients with quantified MLS (i.e., all but the NINDS subjects) into strata based on the following levels of shift: 0mm (n = 944), >0–2mm (n=86), >2–4mm (n=123), >4–6 mm (n=77), >6–8 mm (n=43), >8–10mm (n=32) and >10 mm (n=64).
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8

Comparative Bone Microstructure Analysis

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Mouse femurs from different ages of WT, Rage AHA/+ , Rage AHA/AHA , Rage +/-and Rage -/-mice were harvested, fixed for 48 hours in 10% neutral buffered formalin. A quantitative analysis of the gross bone morphology and microarchitecture was performed using ScanCo microCT 100 system (University at Buffalo). 3D reconstruction and bone microarchitecture analysis were performed using AnalyzePro (AnalyzeDirect Inc).
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9

3D Segmentation of Pelvic Anatomy

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Raw DICOM scans were imported into AnalyzePro (AnalyzeDirect, Overland Park, KS) for review and segmentation of the pelvis, femur, gluteus maximus, and subcutaneous fat. Segmentation was performed under the supervision of an experienced radiographer (BLINDED FOR REVIEW). Skin was included within the subcutaneous fat segmentation when visible, since the scan resolution did not allow for separate segmentation of the two. Point clouds of the 3D segmented surfaces of the bones, muscle, and fat were exported for further analysis in Matlab R2016 (MathWorks, Natick, MA). The peak of the ischial tuberosity and the most inferior point of the greater trochanter when seated were manually identified by a trained student (BLINDED FOR REVIEW) and a radiographer (BLINDED FOR REVIEW), and consensus was reached with regards to the locations.
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