The great success of single-particle electron cryo-microscopy (cryoEM) during the last decade has involved the development of powerful new computer programs and packages that guide the user along a recommended processing workflow, in which the wisdom and choices made by the developers help everyone, especially new users, to obtain excellent results. The ability to carry out novel, non-standard or unusual combinations of image-processing steps is sometimes compromised by the convenience of a standard procedure. Some of the older programs were written with great flexibility and are still very valuable. Among these, the original MRC image-processing programs for structure determination by 2D crystal and helical processing alongside general-purpose utility programs such as Ximdisp, label, imedit and twofile are still available. This work describes an updated version of the MRC software package (MRC2020) that is freely available from CCP-EM. It includes new features and improvements such as extensions to the MRC format that retain the versatility of the package and make it particularly useful for testing novel computational procedures in cryoEM.
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http://dx.doi.org/10.1107/S2052252523006309 | DOI Listing |
Bone Joint J
January 2025
Division of Informatics, Imaging & Data Sciences, The University of Manchester, Manchester, UK.
Aims: The aims of this study were to develop an automatic system capable of calculating four radiological measurements used in the diagnosis and monitoring of cerebral palsy (CP)-related hip disease, and to demonstrate that these measurements are sufficiently accurate to be used in clinical practice.
Methods: We developed a machine-learning system to automatically measure Reimer's migration percentage (RMP), acetabular index (ACI), head shaft angle (HSA), and neck shaft angle (NSA). The system automatically locates points around the femoral head and acetabulum on pelvic radiographs, and uses these to calculate measurements.
Zebrafish
December 2024
Department of Medicine, Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.
Zebrafish larvae are used to model the pathogenesis of multiple bacteria. This transparent model offers the unique advantage of allowing quantification of fluorescent bacterial burdens (fluorescent pixel counts [FPC]) by facile microscopical methods, replacing enumeration of bacteria using time-intensive plating of lysates on bacteriological media. Accurate FPC measurements require laborious manual image processing to mark the outside borders of the animals so as to delineate the bacteria inside the animals from those in the culture medium that they are in.
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December 2024
From the Department of Radiology, University of Washington School of Medicine, Seattle, Wash (A.M.); Department of Radiology, Mayo Clinic, Rochester, Minn (L.Y.); Department of Radiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY (J.W.R.); Departments of Radiation Oncology (S.K.) and Abdominal Imaging (M.A.S., J.J.I.R., V.K.W., K.M.E., C.T.J.), The University of Texas MD Anderson Cancer Center, 1400 Pressler St, Unit 1473, Houston, TX 77030-4009; Department of Radiology, Texas Children's Hospital, Houston, Tex (A.M.R.C.); and Department of Radiology, Seoul National University College of Medicine, Seoul, South Korea (J.M.L.).
Sci Rep
November 2024
Department of Mechanical Engineering, University College London, London, UK.
Automated blood vessel segmentation is critical for biomedical image analysis, as vessel morphology changes are associated with numerous pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. Our goal is to provide a foundation on the topic and identify a robust baseline model for application to vascular segmentation using a new imaging modality, Hierarchical Phase-Contrast Tomography (HiP-CT).
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October 2024
Department of Otorhinolaryngology-Head and Neck Surgery, Jeonbuk National University College of Medicine, 20 Geonji-ro, Deokjin-gu, Jeonju, 54907, South Korea.
Due to the development of magnetic resonance (MR) imaging processing technology, image-based identification of endolymphatic hydrops (EH) has played an important role in understanding inner ear illnesses, such as Meniere's disease or fluctuating sensorineural hearing loss. We segmented the inner ear, consisting of the cochlea, vestibule, and semicircular canals, using a 3D-based deep neural network model for accurate and automated EH volume ratio calculations. We built a dataset of MR cisternography (MRC) and HYDROPS-Mi2 stacks labeled with the segmentation of the perilymph fluid space and endolymph fluid space of the inner ear to devise a 3D segmentation deep neural network model.
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