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Sliceomatic 5

Manufactured by Tomovision
Sourced in Canada

SliceOmatic 5.0 is a software package designed for the analysis and visualization of 3D image data. The software provides tools for segmentation, rendering, and quantification of various structures within a 3D dataset.

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17 protocols using sliceomatic 5

1

MRI-based Abdominal Fat Quantification

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All subjects were examined in the supine position with the Achieva 3.0T MRI system (Philips Healthcare, Eindhoven, The Netherlands). A medically trained technician selected one 10-mm slice at the L3 level with good contrast for the PMA and visceral fat area (VFA) measurements using the sliceOmatic 5.0 software (TomoVision, Magog, Canada). The software calculates areas of different tissues and expresses the measurements in cm2 based on the previously reported method (Shen et al., 2004 (link)).
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2

Body Composition Assessment Using CT Scans

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A single axial CT image at the third lumbar vertebra (L3) was used to examine body composition parameters (9 (link)). Body composition parameters were quantified using Slice-O-Matic 5.0 software (TomoVision), based on density thresholds in Hounsfield units (HU); 29 to +150 for SM, −190 to −30 for SAT, and −150 to −50 for VAT. Total cross-sectional areas were measured in cm2 for SM, VAT and SAT and mean HU densities were reported for SMD. Incomplete cross-sectional areas of SM and SAT in CT scans (e.g., due to poor positioning or large body size of the patient) were estimated in MATLAB. Cross-sectional areas were normalized for height squared (m2) to obtain SMI (cm2/m2), subcutaneous adipose tissue index (SATI, cm2/m2) and VAT index (VATI, cm2/m2) (10 (link)). All CT scan analyses were performed by one trained researcher (J.S.F.M.) following a standardized protocol. A small subset (n=30) was analyzed by a second researcher to assess interrater reproducibility by calculating intraclass correlation coefficients (0.992 for SMI, 0.999 for VAT and 0.979 for SAT).
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3

Measuring Visceral Fat Area using MRI

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VFA was quantified using the Achieva 3.0T MRI system (Philips Healthcare, Eindhoven, The Netherlands). All subjects were examined in the supine position by a medically trained technician to select one 10-mm slice at the L3 level with good contrast for the VFA measurements using the sliceOmatic 5.0 software (TomoVision, Magog, Canada). As previously reported, the software calculates the areas of different tissues and expresses the measurements in cm2 [21 (link)].
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4

CT-Derived Body Composition Analysis

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Body composition was assessed by using computed tomography (CT) imaging and sliceOmatic 5.0 software (TomoVision, Magog, Canada).31 Adipose tissue and skeletal muscle mass were quantified on a cross‐sectional CT‐image at the third lumbar (L3) vertebra that was pre‐operatively acquired for diagnostic purposes. Using predefined Hounsfield unit (HU) ranges, the total cross‐sectional area (cm2) of skeletal muscle tissue (−29 to 150 HU), visceral adipose tissue (VAT) (−150 to −50 HU), and subcutaneous tissue (SAT) (−190 to −30 HU) was determined. The radiation attenuation for skeletal muscle was assessed by calculating the average HU value of the total muscle area within the specified range of −29 to 150 HU. The total areas of skeletal muscle, VAT, and SAT were normalized for stature to calculate the L3‐muscle index (L3‐SMI), L3‐VAT index, and L3‐SAT index in cm2/m2. Previously published sex‐specific cut‐off values were used for the CT‐derived body composition parameters.32
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5

Automated Body Composition Analysis

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The CT images were retrieved using DICOM® (Digital Imaging and Communications in Medicine) software. The de-identified CT information was then sent to the University of Alberta in Edmonton, Canada, where body composition analysis was performed using the TomoVision sliceOmatic 5.0 software. This software enables researchers to calculate SMI (as cm2/m2) by measuring the skeletal muscle mass cross-sectional area (cm2) at L3 and then normalizing the results for patient height in meters squared (m2).
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6

Evaluating Sarcopenia in Hospitalized Patients

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All patients received PG-SGA, abdominal CT, anthropometric measurements, laboratory biochemical testing, and bioelectrical impedance analysis (BIA) within 24 h of admission. Age, sex, height, weight, and albumin (ALB), pre-albumin (PA), neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) in the peripheral blood were recorded. BMI was calculated by weight (kg)/ height 2 (m)2. BIA is a technique for measuring body composition using capacitance (Xc) and resistance (R) of biological tissues. In this study, resistance and capacitance were directly measured in ohms at 50 kHz, 800 mA by Inbody S10 (Biospace Co®). As the equation generated an indicator of body composition, phase angle (PhA) (Resistance/Capacitance) * (180/π).
SliceOmatic 5.0 software (TOMOVISION Canada) was used to analyze abdominal CT images on two consecutive planes of the L3 level. The skeletal muscle areas were measured at each plan, and the average was adopted as skeletal muscle mass, including the psoas major, erector spinae, quadratus lumbar muscles, transverse abdominis, external oblique, and internal oblique. Then the L3 SMI was calculated by skeletal muscle area (cm2)/height2(m2).
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7

Analyzing Body Composition using CT Images

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SliceOmatic 5.0 software (TOMOVISION, Canada) was used to analyze abdominal CT images. According to the voxel values, –29 to + 150 Hu was identified as skeletal muscle mass and −190 to −30 Hu was identified as adipose tissue mass. Then, the skeletal muscle area (SMA) and VFA at the third lumbar vertebra were sketched. The SMA includes the psoas major, the erector spinae, the quadratus lumborum, the transverse abdominis, the external oblique, and the internal oblique. The VFA represents the intra-abdominal adipose tissue. Figure 1 displays the diagrammatic sketch illustrating two patients with the same BMI but different body compositions. SMI (cm2/m2) = SMA/height2 (m2).
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8

Prognostic Factors in Colorectal Cancer

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Demographic and clinical variables included age, sex, race, body mass index (BMI), per cent body weight (BW) loss in the 6 months prior to diagnosis, as well as serum albumin, bilirubin, haemoglobin and platelet count at the time of diagnosis. Computed tomography scans at the time of diagnosis were obtained and analysed using sliceOmatic ® 5.0 software (TomoVision, Magog, Canada) to compute skeletal muscle index (SMI), muscle radiation attenuation (MRA), visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT) and intramuscular adipose tissue (IMAT) of axial images at the level of the L3 vertebra. Pathologic variables included tumour stage, tumour size, nodal stage, number of positive lymph nodes, lymph node positivity ratio, margin status, presence of perineural or lymphovascular invasion, and histologic differentiation. Overall survival time (months) from the date of surgery to death was calculated. Vital status was confirmed as of 15 March 2021.
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9

MRI-based Abdominal Adiposity Quantification

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Abdominal MRI examination was performed using a Philips Achieva 3.0-T magnetic resonance imaging system (Philips Medical Systems, Eindhoven, The Netherlands). Breath-hold fast imaging with a 40-ms repetition time, 2-ms echo time, 50-cm field of view, and 256 × 256 matrix was used to acquire the cross-sectional MR images. One 10-mm slice positioned at the L4 level with a clear outline was selected for analysis using SliceOmatic 5.0 software (TomoVision, Magog, Canada) by a medically trained technician. The psoas CSA, SFA, and VFA were measured using the following steps: regional threshold procedures were first applied using the “Region Growing” mode, after which manual delineation was used to draw borders among different tissues in the “edit mode” when necessary (10 (link)). The software calculated different colored areas and expressed the measurements in cm2. VFA≥80cm2 was defined as visceral obesity.
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10

Quantifying Body Composition from CT Images

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Cross-sectional areas (cm2) of skeletal muscle, VAT, and SAT were assessed using standard radiodensity thresholds measured in Hounsfield units (HU) in preoperative CT images at the level of the 3rd lumbar vertebrae using Slice-O-Matic 5.0 (Tomovision, Montreal, Canada). For skeletal muscle, the threshold values were between − 29 and + 150 HU, for VAT between − 150 and − 50 HU, and for SAT between − 190 and − 30 HU [22 (link), 23 (link)]. The skeletal muscle cross-sectional area was adjusted for height squared (cm2/m2) to calculate skeletal muscle index (SMI). SMR was assessed as the mean radiodensity of the total skeletal muscle cross-sectional area at the level of the 3rd lumbar vertebrae.
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