Osirix md software

Manufactured by Pixmeo

Sourced in Switzerland, United States

OsiriX MD is a medical imaging software application designed for digital imaging and communications in medicine (DICOM) image visualization and analysis. It allows users to view, process, and manage medical images from various modalities, including CT, MRI, PET, and others. The software's core function is to provide a comprehensive platform for medical professionals to access, manipulate, and interpret medical images in a efficient and user-friendly manner.

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Lab products found in correlation

Ingenia 3.0t, by Philips (4 mentions) Multiscan lfer 150 pet ct scanner, by Mediso (3 mentions) Imaris software, by Zeiss (2 mentions) Premiere pro cc, by Adobe (2 mentions) Avizo 3d software, by Thermo Fisher Scientific (1 mentions) Somatom definition as, by Siemens (1 mentions) Nanozoomer, by Hamamatsu Photonics (1 mentions) Ndp view2, by Hamamatsu Photonics (1 mentions) Latheta lct 200, by Hitachi (1 mentions) Analyze 12, by PerkinElmer (1 mentions) Quantum fx, by PerkinElmer (1 mentions) Magnetom allegra, by Siemens (1 mentions) Cmr42, by Circle Cardiovascular Imaging (1 mentions)

Spelling variants of this product

OsiriX (197 citations) OsiriX software (85 citations) OsiriX MD (65 citations) OsiriX MD Imaging Software (5 citations) OsiriX MD image processing software (2 citations)

22 protocols using osirix md software

Standardized MRI Protocol for Knee Assessment

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The study was evaluated on iMac pro (Apple, Cupertino, USA) using the FDA-approved OsiriX MD software (version 11.0, Pixmeo SARL, Bernex, Switzerland). All MRI studies were irreversibly anonymized. MRI were performed on a 3.0T scanner (Ingenia 3.0T, Philips, Amsterdam, Netherlands) or on a 1.5T GE scanner (SIGNA, GE, Milwaukee, USA) GE instrument at different facilities located in clinical hospitals and private facilities in Zamość, Elbląg, Jelenia Góra, and Bielsko-Biała. The MRI protocols were standardized in all MR laboratories. Studies with differing protocols were excluded.
The following diagnostic sequence protocol was used in the study: axial, sagittal, and coronal PD FS; sagittal and coronal T1 (all with a slice thickness of 3 mm); and 3D high-resolution PD FS with a slice thickness from 0.8 to 1 mm. The same protocol was used in each diagnostic facility. Sequence parameters were in accordance with the European Society of Sport Traumatology, Knee Surgery & Arthroscopy (ESSKA) (Table 2) [20 ]. All images were assessed by an experienced musculoskeletal radiologist.

Sieroń D., Jabłońska I., Niemiec P., Lukoszek D., Szyluk K., Platzek I., Meusburger H., Delimpasis G, & Christe A. (2022). Correlation of Patellofemoral Chondromalacia and Body Mass Index (BMI) in Relation to Sex and Age Analysis of 1.5T and 3.0T Magnetic Resonance (MR) Images Using the Outerbridge Scale. Medical Science Monitor : International Medical Journal of Experimental and Clinical Research, 28, e937246-1-e937246-11.

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Knee MRI Cartilage Chondromalacia Assessment

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Among patients undergoing knee MRI between 2018 and 2019, 481 patients were retrospectively selected from the archives of community and clinical hospitals as well as private clinics in Zamość Elblag, Jelenia Góra and Bielsko-Biala (Poland) based on the inclusion and exclusion criteria listed below. The study was performed according to the STROBE guidelines. A number of 120–121 patients for each of four age groups were selected: <30 years (120); 30–45 years (120); 46–60 years (120); >60 years (121). Demographic data were retrieved from the MRI safety questionnaires of the corresponding clinics (age, sex, height, weight and BMI). The MR images used for this study had been acquired on either 1.5 T (SIGNA, GE, Milwaukee, WI, USA) or 3 T (Ingenia 3.0 T, Philips, Amsterdam, Netherlands) scanners using the following diagnostic sequence protocols: axial, sagittal and coronal PD FS, sagittal and coronal T1 (all with a slice thickness of 3 mm), 3D high-resolution PD FS with a slice thickness from 0.8 to 1 mm. All MRI data were irreversibly anonymized, and evaluated using iMac pro (Apple, Cupertino, CA, USA) with FDA-approved OsiriX MD software (version 11.0, Pixmeo SARL, Bernex, Switzerland). The radiological evaluation of cartilage chondromalacia included the medial, lateral and retropatellar compartments of the knee joint.

Primetis E., Drakopoulos D., Sieron D., Meusburger H., Szyluk K., Niemiec P., Obmann V.C., Peters A.A., Huber A.T., Ebner L., Delimpasis G, & Christe A. (2022). Knee Diameter and Cross-Sectional Area as Biomarkers for Cartilage Knee Degeneration on Magnetic Resonance Images. Medicina, 59(1), 27.

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Comprehensive Aortic Imaging Protocol

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Diagnosis was confirmed by multislice high-resolution spiral computed tomography angiography (CTA). Multiplanar and three-dimensional workstation reconstructions were used to evaluate aortic pathology. Standard of care CTA is baseline for case planning, before discharge, 3 months, 6 months and yearly thereafter. In Mainz, images are evaluated with Sectra Workstation IDS 7 (Sectra AB, Linkoeping, Sweden) with automatic generation of centerline of flow (CLF); in Tübingen, with Osirix MD software (Pixmeo, Bernex, Switzerland). Case planning included access vessel anatomy evaluation including diameter (lowest diameter between the femoral access artery and the aortic bifurcation on the access site); calcification (significant if vessel diameter area shows a stenosis > 50%); and tortuosity index of both thoracic aorta and iliac arteries (ratios between CLF distance [thoracic aorta: from the fourth thoracic vertebrae to the offspring of the celiac trunk; iliac arteries: from the aortic bifurcation to the offspring of inferior epigastric arteries) and the shortest distance between the same measurements). Tortuosity index values were interpreted as mild (<1.1), moderate (1.11–1.18) or severe (≥1.19). Aortic arch classification was performed in respect to STORAGE guidelines and the Modified Arch Landing Areas Nomenclature (MALAN) classification based on hemodynamic features [15 (link)].

El Beyrouti H., Lescan M., Doemland M., Mustafi M., Jungmann F., Jorg T., Halloum N, & Dorweiler B. (2020). Early results of a low-profile stent-graft for thoracic endovascular aortic repair. PLoS ONE, 15(11), e0240560.

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Longitudinal FDG PET/CT Imaging of Tuberculosis

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Radiolabeled 2-deoxy-2-(¹⁸F)fluoro-d-glucose (FDG) PET/CT imaging was performed 4, 8 and 12 weeks after Mtb challenge. Imaging was performed using a MultiScan LFER-150 PET/CT scanner (Mediso Medical Imaging Systems) housed within our biosafety level 3 facility as previously described^{66 (link),67 (link)}. Co-registered PET/CT images were analysed using OsiriX MD software (version 12.5.2, Pixmeo) to enumerate granulomas and to calculate the total FDG avidity of the lungs, exclusive of lymph nodes, which are a quantitative measure of total inflammation in the lungs^{66 (link),68}. For historical controls, PET/CT scans were performed using a microPET Focus 220 preclinical PET scanner (Siemens Molecular Solutions) and a clinical eight-slice helical CT scanner (NeuroLogica Corporation)⁶⁸. Thoracic lymphadenopathy and extrapulmonary dissemination of Mtb to the spleen and/or liver were also assessed qualitatively on these scans.

Larson E.C., Ellis-Connell A.L., Rodgers M.A., Gubernat A.K., Gleim J.L., Moriarty R.V., Balgeman A.J., Ameel C.L., Jauro S., Tomko J.A., Kracinovsky K.B., Maiello P., Borish H.J., White A.G., Klein E., Bucsan A.N., Darrah P.A., Seder R.A., Roederer M., Lin P.L., Flynn J.L., O’Connor S.L, & Scanga C.A. (2023). Intravenous Bacille Calmette–Guérin vaccination protects simian immunodeficiency virus-infected macaques from tuberculosis. Nature Microbiology, 8(11), 2080-2092.

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Longitudinal PET/CT Imaging of Tuberculosis

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Radiolabeled 2-deoxy-2-(¹⁸F)fluoro-d-glucose (FDG) PET/CT was performed just prior to Mtb infection and then monthly after Mtb infection. Imaging was performed using a MultiScan LFER-150 PET/CT scanner (Mediso Medical Imaging Systems) housed within our BSL3 facility as previously described (92 (link), 93 (link)). Co-registered PET/CT images were analyzed using OsiriX MD software (version 12.5.2, Pixmeo) to enumerate granulomas and to calculate the total FDG avidity of the lungs, exclusive of lymph nodes, which is a quantitative measure of total inflammation in the lungs (92 (link), 94 (link)). Thoracic lymphadenopathy and extrapulmonary dissemination of Mtb to the spleen and/or liver were also assessed qualitatively on these scans.

Larson E.C., Ellis A.L., Rodgers M.A., Gubernat A.K., Gleim J.L., Moriarty R.V., Balgeman A.J., Menezes Y.K., Ameel C.L., Fillmore D.J., Pergalske S.M., Juno J.A., Maiello P., White A.G., Borish H.J., Godfrey D.I., Kent S.J., Ndhlovu L.C., O’Connor S.L, & Scanga C.A. (2023). Host Immunity to Mycobacterium tuberculosis Infection Is Similar in Simian Immunodeficiency Virus (SIV)-Infected, Antiretroviral Therapy-Treated and SIV-Naïve Juvenile Macaques. Infection and Immunity, 91(5), e00558-22.

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PET/CT Imaging of Infectious Diseases in Mice

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PET/CT images of Leishmania-infected mice (BALB/c, 8 week old, male, 17.5–20.8 g, n = 4), SFTSV-infected mice (IFNAR-KO, 8 week old, male,
16.3–26.5 g, n = 4), and control mice injected
with sterile medium (IFNAR-KO, 8 week old, male, 22.6–29.4
g, n = 4) were acquired with a Triumph combined PET/SPECT/CT
system (TriFoil Imaging Inc., CA). Generator-eluted ⁶⁸Ga-citrate
was diluted with 1.3× volume of H₂O to adjust the
osmotic pressure. Each mouse was administered ⁶⁸Ga-citrate
(4.5–6.0 MBq) or ¹⁸F-FDG (10.5–12.5 MBq)
in the tail vein. The mice were anesthetized with 1.5% isoflurane,
and the CT acquisitions were performed for anatomical reference. Subsequently,
1 h ⁶⁸Ga PET acquisitions commenced 2 h after injection
of ⁶⁸Ga-citrate or 30 min ¹⁸F acquisitions commenced
30 min after injection of ¹⁸F-FDG. The PET data were reconstructed
using a three-dimensional maximum-likelihood expectation maximization
algorithm (Iteration30). Acquired PET and CT data were processed,
and PET images were quantified using OsiriX MD software (Pixmeo, Geneva,
Switzerland). Tracer uptake was expressed as the standardized uptake
value (SUV), which was calculated as follows

Fuchigami T., Ono H., Oyadomari K., Iwatake M., Hayasaka D., Akbari M., Yui K., Nishi K., Kudo T., Yoshida S., Haratake M, & Nakayama M. (2017). Development of a 68Ge/68Ga Generator System Using Polysaccharide Polymers and Its Application in PET Imaging of Tropical Infectious Diseases. ACS Omega, 2(4), 1400-1407.

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X-ray CT Imaging and Analysis of Savonnières Rock Samples

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The Savonnières rock samples were x-ray CT imaged using a Siemens scanner SOMATOM Definition AS at an energy of 140 kV and current of 500 mA. X-ray CT transversal images were acquired with the best field of view capable to achieve a voxel size of 0.1 × 0.1 × 0.1 mm. Avizo 3D software from Thermofisher and Osirix MD software from Pixmeo were used to process the X-ray images and generate 2D and 3D views to observe the samples' inner structure before and after testing. After applying non-local mean filtering to remove some noise from the images, a single threshold on the CT histogram with a CT number less than 500 HU was used to segment the pores/open structures.
A low pass filter was applied to the segmented image to remove small pores and artefacts on the images. In order to only see generated fractures/faults from the geomechanical experiment, an island removal of 50 pixels (i.e., ≤ 5 mm object size) was applied to remove most pores in Savonnieres sample (pore diameter « 5 mm diameter) and keep only the main big size open structures (i.e., >5 mm) like faults [51 ]. A volume rendering of the segmented images was finally produced on Osirix MD software to visualise the whole structures and match the orientation of the visible structures on the surface of the plug.

da Silva Falcão B., Giwelli A., Nogueira Kiewiet M., Banks S., Yabesh G., Esteban L., Kiewiet L., Yekeen N., Kovalyshen Y., Monmusson L., Al-Yaseri A., Keshavarz A, & Iglauer S. (2023). Strain measurement with multiplexed FBG sensor arrays: An experimental investigation. Heliyon, 9(8), e18652.

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Quantitative Histomorphometric Analysis of Bone

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Photographs of HE and TRAP staining were taken using a virtual slide scanner (NanoZoomer^®, Hamamatsu Pho-tonics K.K., Hamamatsu, Japan) at 25× and 200× magnification. The pixel size of each picture was adjusted to 1920 × 1128 (pixels) and analyzed using NDP. View 2 software (Hamamatsu Pho-tonics K.K., Hamamatsu, Japan).
Micro-CT volumetric analysis was performed using OsiriX MD software (Pixmeo, Switzerland).
For histomorphometric analysis, the area of newly formed bone and total was selected using Adobe Photoshop CS 5.1. Each region of the photograph was quantified using the ImageJ software (National Institutes of Health, Bethesda, MD, USA).

Shiwaku Y., Hamai R., Sato S., Sakai S., Tsuchiya K., Baba K., Takahashi T, & Suzuki O. (2021). Bone Tissue Response to Different Grown Crystal Batches of Octacalcium Phosphate in Rat Long Bone Intramedullary Canal Area. International Journal of Molecular Sciences, 22(18), 9770.

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X-Ray Micro-CT Imaging of Zebrafish

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WT and stm mutant adult zebrafish were fixed with 70% ethanol and stored in 70% ethanol. The heads of zebrafish were scanned using an X-ray micro-CT device (ScanX- mate-E090S105, Comscantechno Co., Ltd., Japan) at a tube voltage peak of 60 kVp and a tube current of 100 μA. The sample was rotated 360° in steps of 0.24°, generating 1500 projection images of 992 × 992 pixels. The micro-CT data were reconstructed at an isotropic resolution of 13.3 × 13.3 × 13.3 μm. Three-dimensional tomographic images were obtained using OsiriX MD software (version 9.0, Pixmeo, SARL, Switzerland) and Imaris software (version 9.1, Carl Zeiss Microscopy Co., Ltd.). Supplementary video (Supplementary video 1, see section on supplementary materials given at the end of this article) was edited using Adobe Premiere Pro CC (Adobe Systems Co., Ltd., Japan).

Pachoensuk T., Fukuyo T., Rezanujjaman M., Wanlada K., Yamamoto C., Maeno A., Rahaman M.M., Ali M.H, & Tokumoto T. (2021). Zebrafish stm is involved in the development of otoliths and of the fertilization envelope. Reproduction & Fertility, 2(1), 7-16.

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Lymph Node Segmentation from CT Images

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The study workflow is shown in Figure 4. Three CT images, namely the image showing the largest cross-sectional area of the targeted LN and the adjacent images (one cranial and one caudal image), were obtained using OsirixMD software (Pixmeo, Bernex, Switzerland). The margin of the LNs on the selected images were contoured as close as possible by a single radiologist (**blinded** with 9 years of experience).
All images were resized to 300 × 300 pixels. All images were normalized and divided by 255 before the augmentation. The resized images were augmented by horizontal flip, vertical flip, width shift, and height shift. The programming language used for augmentation was Python 3.6 (https://www.python.org).

Tomita H., Yamashiro T., Heianna J., Nakasone T., Kobayashi T., Mishiro S., Hirahara D., Takaya E., Mimura H., Murayama S, & Kobayashi Y. (2021). Deep Learning for the Preoperative Diagnosis of Metastatic Cervical Lymph Nodes on Contrast-Enhanced Computed ToMography in Patients with Oral Squamous Cell Carcinoma. Cancers, 13(4), 600.

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