Fabric Image Representation Encoding Networks for Large-scale 3D Medical Image Analysis

Deep neural networks are parameterised by weights that encode feature representations, whose performance is dictated through generalisation by using large-scale feature-rich datasets. The lack of large-scale labelled 3D medical imaging datasets restrict constructing such generalised networks. In this work, a novel 3D segmentation network, Fabric Image Representation Networks (FIRENet), is proposed to extract and encode generalisable feature representations from multiple medical image datasets in a large-scale manner. FIRENet learns image specific feature representations by way of 3D fabric network architecture that contains exponential number of sub-architectures to handle various protocols and coverage of anatomical regions and structures. The fabric network uses Atrous Spatial Pyramid Pooling (ASPP) extended to 3D to extract local and image-level features at a fine selection of scales. The fabric is constructed with weighted edges allowing the learnt features to dynamically adapt to the training data at an architecture level. Conditional padding modules, which are integrated into the network to reinsert voxels discarded by feature pooling, allow the network to inherently process different-size images at their original resolutions. FIRENet was trained for feature learning via automated semantic segmentation of pelvic structures and obtained a state-of-the-art median DSC score of 0.867. FIRENet was also simultaneously trained on MR (Magnatic Resonance) images acquired from 3D examinations of musculoskeletal elements in the (hip, knee, shoulder) joints and a public OAI knee dataset to perform automated segmentation of bone across anatomy. Transfer learning was used to show that the features learnt through the pelvic segmentation helped achieve improved mean DSC scores of 0.962, 0.963, 0.945 and 0.986 for automated segmentation of bone across datasets.Comment: 12 pages, 10 figure

A review of segmentation and deformable registration methods applied to adaptive cervical cancer radiation therapy treatment planning

Objective: Manual contouring and registration for radiotherapy treatment planning and online adaptation for cervical cancer radiation therapy in computed tomography (CT) and magnetic resonance images (MRI) are often necessary. However manual intervention is time consuming and may suffer from inter or intra-rater variability. In recent years a number of computer-guided automatic or semi-automatic segmentation and registration methods have been proposed. Segmentation and registration in CT and MRI for this purpose is a challenging task due to soft tissue deformation, inter-patient shape and appearance variation and anatomical changes over the course of treatment. The objective of this work is to provide a state-of-the-art review of computer-aided methods developed for adaptive treatment planning and radiation therapy planning for cervical cancer radiation therapy. Methods: Segmentation and registration methods published with the goal of cervical cancer treatment planning and adaptation have been identified from the literature (PubMed and Google Scholar). A comprehensive description of each method is provided. Similarities and differences of these methods are highlighted and the strengths and weaknesses of these methods are discussed. A discussion about choice of an appropriate method for a given modality is provided. Results: In the reviewed papers a Dice similarity coefficient of around 0.85 along with mean absolute surface distance of 2-4. mm for the clinically treated volume were reported for transfer of contours from planning day to the treatment day. Conclusions: Most segmentation and non-rigid registration methods have been primarily designed for adaptive re-planning for the transfer of contours from planning day to the treatment day. The use of shape priors significantly improved segmentation and registration accuracy compared to other models

Validation of virtual water phantom software for pre-treatment verification of single-isocenter multiple-target stereotactic radiosurgery

Objectiu múltiple; SRS; Fantasma virtualObjetivo múltiple; SRS; Fantasma virtualMultiple‐target; SRS; Virtual phantomThe aim of this study was to benchmark the accuracy of the VIrtual Phantom Epid dose Reconstruction (VIPER) software for pre-treatment dosimetric verification of multiple-target stereotactic radiosurgery (SRS). VIPER is an EPID-based method to reconstruct a 3D dose distribution in a virtual phantom from in-air portal images. Validation of the VIPER dose calculation was assessed using several MLC-defined fields for a 6 MV photon beam. Central axis percent depth doses (PDDs) and output factors were measured with an ionization chamber in a water tank, while dose planes at a depth of 10 cm in a solid flat phantom were acquired with radiochromic films. The accuracy of VIPER for multiple-target SRS plan verification was benchmarked against Monte Carlo simulations. Eighteen multiple-target SRS plans designed with the Eclipse treatment planning system were mapped to a cylindrical water phantom. For each plan, the 3D dose distribution reconstructed by VIPER within the phantom was compared with the Monte Carlo simulation, using a 3D gamma analysis. Dose differences (VIPER vs. measurements) generally within 2% were found for the MLC-defined fields, while film dosimetry revealed gamma passing rates (GPRs) ≥95% for a 3%/1 mm criteria. For the 18 multiple-target SRS plans, average 3D GPRs greater than 93% and 98% for the 3%/2 mm and 5%/2 mm criteria, respectively. Our results validate the use of VIPER as a dosimetric verification tool for pre-treatment QA of single-isocenter multiple-target SRS plans. The method requires no setup time on the linac and results in an accurate 3D characterization of the delivered dose

Gender and Videogames: The political valency of Lara Croft

The Face: Is Lara a feminist icon or a sexist fantasy? Toby Gard: Neither and a bit of both. Lara was designed to be a tough, self-reliant, intelligent woman. She confounds all the sexist cliches apart from the fact that she’s got an unbelievable figure. Strong, independent women are the perfect fantasy girls—the untouchable is always the most desirable (Interview with Lara’s creator Toby Gard in The Face magazine, June 1997)

Development of a Geographic Information System for Natural Resources and Recreational Facilities

unpublishednot peer reviewedOpe

Intensity-based dual model method for generation of synthetic CT images from standard T2-weighted MR images - Generalized technique for four different MR scanners

Background and purpose: Recent studies have shown that it is possible to conduct entire radiotherapy treatment planning (RTP) workflow using only MR images. This study aims to develop a generalized intensity-based method to generate synthetic CT (sCT) images from standard T2-weighted (T2(W)) MR images of the pelvis. Materials and methods: This study developed a generalized dual model HU conversion method to convert standard T2(W) MR image intensity values to synthetic HU values, separately inside and outside of atlas-segmented bone volume contour. The method was developed and evaluated with 20 and 35 prostate cancer patients, respectively. MR images with scanning sequences in clinical use were acquired with four different MR scanners of three vendors. Results: For the generated synthetic CT (sCT) images of the 35 prostate patients, the mean (and maximal) HU differences in soft and bony tissue volumes were 16 +/- 6 HUs (34 HUs) and -46 +/- 56 HUs (181 HUs), respectively, against the true CT images. The average of the PTV mean dose difference in sCTs compared to those in true CTs was -0.6 +/- 0.4% (-1.3%). Conclusions: The study provides a generalized method for sCT creation from standard T2(W) images of the pelvis. The method produced clinically acceptable dose calculation results for all the included scanners and MR sequences. (c) 2017 Elsevier B.V. All rights reserved.Peer reviewe

Commissioning and quality assurance for VMAT delivery systems: An efficient time-resolved system using real-time EPID imaging.

PURPOSE: An ideal commissioning and quality assurance (QA) program for Volumetric Modulated Arc Therapy (VMAT) delivery systems should assess the performance of each individual dynamic component as a function of gantry angle. Procedures within such a program should also be time-efficient, independent of the delivery system and be sensitive to all types of errors. The purpose of this work is to develop a system for automated time-resolved commissioning and QA of VMAT control systems which meets these criteria. METHODS: The procedures developed within this work rely solely on images obtained, using an electronic portal imaging device (EPID) without the presence of a phantom. During the delivery of specially designed VMAT test plans, EPID frames were acquired at 9.5 Hz, using a frame grabber. The set of test plans was developed to individually assess the performance of the dose delivery and multileaf collimator (MLC) control systems under varying levels of delivery complexities. An in-house software tool was developed to automatically extract features from the EPID images and evaluate the following characteristics as a function of gantry angle: dose delivery accuracy, dose rate constancy, beam profile constancy, gantry speed constancy, dynamic MLC positioning accuracy, MLC speed and acceleration constancy, and synchronization between gantry angle, MLC positioning and dose rate. Machine log files were also acquired during each delivery and subsequently compared to information extracted from EPID image frames. RESULTS: The largest difference between measured and planned dose at any gantry angle was 0.8% which correlated with rapid changes in dose rate and gantry speed. For all other test plans, the dose delivered was within 0.25% of the planned dose for all gantry angles. Profile constancy was not found to vary with gantry angle for tests where gantry speed and dose rate were constant, however, for tests with varying dose rate and gantry speed, segments with lower dose rate and higher gantry speed exhibited less profile stability. MLC positional accuracy was not observed to be dependent on the degree of interdigitation. MLC speed was measured for each individual leaf and slower leaf speeds were shown to be compensated for by lower dose rates. The test procedures were found to be sensitive to 1 mm systematic MLC errors, 1 mm random MLC errors, 0.4 mm MLC gap errors and synchronization errors between the MLC, dose rate and gantry angle controls systems of 1°. In general, parameters measured by both EPID and log files agreed with the plan, however, a greater average departure from the plan was evidenced by the EPID measurements. CONCLUSION: QA test plans and analysis methods have been developed to assess the performance of each dynamic component of VMAT deliveries individually and as a function of gantry angle. This methodology relies solely on time-resolved EPID imaging without the presence of a phantom and has been shown to be sensitive to a range of delivery errors. The procedures developed in this work are both comprehensive and time-efficient and can be used for streamlined commissioning and QA of VMAT delivery systems

Apicomplexan Parasites Co-Opt Host Calpains to Facilitate Their Escape from Infected Cells

Apicomplexan parasites, including Plasmodium falciparum and Toxoplasma gondii (the causative agents of malaria and toxoplasmosis, respectively), are responsible for considerable morbidity and mortality worldwide. These pathogenic protozoa replicate within an intracellular vacuole inside of infected host cells, from which they must escape to initiate a new lytic cycle. By integrating cell biological, pharmacological, and genetic approaches, we provide evidence that both Plasmodium and Toxoplasma hijack host cell calpain proteases to facilitate parasite egress. Immunodepletion or inhibition of calpain-1 in hypotonically lysed and resealed erythrocytes prevented the escape of P. falciparum parasites, which was restored by adding purified calpain-1. Similarly, efficient egress of T. gondii from mammalian fibroblasts was blocked by either small interfering RNA– mediated suppression or genetic deletion of calpain activity and could be restored by genetic complementation

Verification of stereotactic radiosurgery plans for multiple brain metastases using a virtual phantom-based procedure

Background: The purpose of this study was to describe the use of the VIPER software for patient-specific quality assurance (PSQA) of single-isocenter multitarget (SIMT) stereotactic radiosurgery (SRS) plans. Materials and methods: Twenty clinical of intensity-modulated (IMRT) SIMT SRS plans were reviewed. A total of 88 brain metastases were included. Number of lesions per plan and their individual volumes ranged from 2 to 35 and from 0.03 to 32.8 cm3, respectively. Plans were designed with the Eclipse system, and delivered using a Varian CLINAC linac. SRS technique consisted of non-coplanar static-field sliding-window IMRT. Each plan was mapped onto a virtual cylindrical water phantom (VCP) in the Eclipse to calculate a 3D dose distribution (verification plan). The VIPER software reconstructed the 3D dose distribution inside the VCP from the acquired in-air electronic portal image device (EPID) images of the treatment fields. A 3D gamma analysis was used to compare the reconstructed doses to the Eclipse planned doses on the VCP. Gamma passing rates (GPRs) were calculated using 3% global/2 mm criteria and dose thresholds ranged from 10% to 90% of the maximum dose. Results: The averages (± 1 SD) of the 3D GPRs over the 20 SRS plans were: 99.9 ± 0.2%, 99.7 ± 0.3%, 99.6 ± 0.5%, 99.3 ± 0.9%,99.1 ± 1.6%, 99.0 ± 1.6%, and 98.5 ± 3.3%, for dose thresholds of 10%, 20%, 30%, 50%, 70%, 80% and 90% respectively. Conclusions: This work shows the feasibility of the VIPER software for PSQA of SIMT SRS plans, being a reliable alternative to commercially available 2D detector arrays