MBAPose: Mask and Bounding-Box Aware Pose Estimation of Surgical Instruments with Photorealistic Domain Randomization

Surgical robots are controlled using a priori models based on robots' geometric parameters, which are calibrated before the surgical procedure. One of the challenges in using robots in real surgical settings is that parameters change over time, consequently deteriorating control accuracy. In this context, our group has been investigating online calibration strategies without added sensors. In one step toward that goal, we have developed an algorithm to estimate the pose of the instruments' shafts in endoscopic images. In this study, we build upon that earlier work and propose a new framework to more precisely estimate the pose of a rigid surgical instrument. Our strategy is based on a novel pose estimation model called MBAPose and the use of synthetic training data. Our experiments demonstrated an improvement of 21 % for translation error and 26 % for orientation error on synthetic test data with respect to our previous work. Results with real test data provide a baseline for further research.Comment: 8 pages, submitted to IROS202

Single-Shot Pose Estimation of Surgical Robot Instruments' Shafts from Monocular Endoscopic Images

Surgical robots are used to perform minimally invasive surgery and alleviate much of the burden imposed on surgeons. Our group has developed a surgical robot to aid in the removal of tumors at the base of the skull via access through the nostrils. To avoid injuring the patients, a collision-avoidance algorithm that depends on having an accurate model for the poses of the instruments' shafts is used. Given that the model's parameters can change over time owing to interactions between instruments and other disturbances, the online estimation of the poses of the instrument's shaft is essential. In this work, we propose a new method to estimate the pose of the surgical instruments' shafts using a monocular endoscope. Our method is based on the use of an automatically annotated training dataset and an improved pose-estimation deep-learning architecture. In preliminary experiments, we show that our method can surpass state of the art vision-based marker-less pose estimation techniques (providing an error decrease of 55% in position estimation, 64% in pitch, and 69% in yaw) by using artificial images.Comment: Accepted on ICRA 2020, 7 page

Implementation of a novel PCR based method for detecting malaria parasites from naturally infected mosquitoes in Papua New Guinea

<p>Abstract</p> <p>Background</p> <p>Detection of <it>Plasmodium species </it>in mosquitoes is important for designing vector control studies. However, most of the PCR-based detection methods show some potential limitations. The objective of this study was to introduce an effective PCR-based method for detecting <it>Plasmodium vivax </it>and <it>Plasmodium falciparum </it>from the field-caught mosquitoes of Papua New Guinea.</p> <p>Methods</p> <p>A method has been developed to concurrently detect mitochondrial cytochrome b (<it>Cyt b</it>) of four human <it>Plasmodium </it>species using PCR (<it>Cytb</it>-PCR). To particularly discriminate <it>P. falciparum </it>from <it>P. vivax</it>, <it>Plasmodium ovale </it>and <it>Plasmodium malariae</it>, a polymerase chain reaction-repeated fragment length polymorphism (PCR-RFLP) has further been developed to use with this method. However, due to limited samples number of <it>P. ovale </it>and <it>P. malariae</it>; this study was mainly confined to <it>P. vivax </it>and <it>P. falciparum</it>. The efficiency of <it>Cytb</it>-PCR was evaluated by comparing it with two 'gold standards' enzyme linked immunosorbent assay specific for circumsporozoite protein (CS-ELISA) using artificially infected mosquitoes; and nested PCR specific for small subunit ribosomal RNA (<it>SSUrRNA</it>) using field caught mosquitoes collected from three areas (Kaboibus, Wingei, and Jawia) of the East Sepic Province of Papua New Guinea.</p> <p>Results</p> <p>A total of 90 mosquitoes were artificially infected with three strains of <it>Plasmodium</it>: <it>P. vivax-</it>210 (<it>n </it>= 30), <it>P. vivax</it>-247 (<it>n </it>= 30) and <it>P. falciparum </it>(<it>n </it>= 30). These infected mosquitoes along with another 32 unfed mosquitoes were first checked for the presence of <it>Plasmodium </it>infection by CS-ELISA, and later the same samples were compared with the <it>Cytb</it>-PCR. CS-ELISA for <it>P. vivax</it>-210, <it>P. vivax</it>-247 and <it>P. falciparum </it>detected positive infection in 30, 19 and 18 mosquitoes respectively; whereas <it>Cytb</it>-PCR detected 27, 16 and 16 infections, respectively. The comparison revealed a close agreement between the two assays (κ = 0.862, 0.842 and 0.894, respectively for Pv-210, Pv-247 and <it>P. falciparum </it>groups). It was found that the eight CS-ELISA-positive mosquitoes detected negative by <it>Cytb</it>-PCR were false-positive results. The lowest detection limit of this <it>Cytb</it>-PCR was 10 sporozoites. A highly concordance result was also found between nested PCR and <it>Cytb</it>-PCR using 107 field caught mosquitoes, and both tests concordantly detected <it>P. falciparum </it>in an <it>Anopheles punctulatus </it>mosquito collected from Kaboibus. Both tests thus suggested an overall sporozoite rate of 0.9% (1/107) in the study areas. Subsequently, PCR-RFLP efficiently discriminated <it>P. falciparum </it>from <it>P. vivax </it>for all of the <it>Cytb</it>-PCR positive samples.</p> <p>Conclusion</p> <p>A single step PCR based method has been introduced here that is highly sensitive, efficient and reliable for identifying <it>P. vivax </it>and <it>P. falciparum </it>from mosquitoes. The reliability of the technique was confirmed by its ability to detect <it>Plasmodium </it>as efficiently as those of CS-ELISA and nested PCR. Application of the assay offers the opportunity to detect vector species of Papua New Guinea and may contribute for designing further vector control programmes.</p

Genetic diversity in two sibling species of the Anopheles punctulatus group of mosquitoes on Guadalcanal in the Solomon Islands

<p>Abstract</p> <p>Background</p> <p>The mosquito <it>Anopheles irenicus</it>, a member of the <it>Anopheles punctulatus </it>group, is geographically restricted to Guadalcanal in the Solomon Islands. It shows remarkable morphological similarities to one of its sibling species, <it>An. farauti sensu stricto </it>(<it>An. farauti s.s</it>.), but is dissimilar in host and habitat preferences. To infer the genetic variations between these two species, we have analyzed mitochondrial <it>cytochrome oxidase subunit II </it>(<it>COII</it>) and nuclear ribosomal <it>internal transcribed spacer 2 </it>(<it>ITS2</it>) sequences from Guadalcanal and from one of its nearest neighbours, Malaita, in the Solomon Islands.</p> <p>Results</p> <p><it>An. farauti s.s</it>. was collected mostly from brackish water and by the human bait method on both islands, whereas <it>An. irenicus </it>was only collected from fresh water bodies on Guadalcanal Island. <it>An. irenicus </it>is distributed evenly with <it>An. farauti s.s</it>. (Φ_SC= 0.033, 0.38%) and its range overlaps in three of the seven sampling sites. However, there is a significant population genetic structure between the species (Φ_CT= 0.863, <it>P </it>< 0.01; Φ_ST= 0.865, <it>P </it>< 0.01 and <it>F</it>_ST= 0.878, <it>P </it>< 0.01). Phylogenetic analyses suggest that <it>An. irenicus </it>is a monophyletic species, not a hybrid, and is closely related to the <it>An. farauti s.s</it>. on Guadalcanal. The time estimator suggests that <it>An. irenicus </it>diverged from the ancestral <it>An. farauti s.s</it>. on Guadalcanal within 29,000 years before present (BP). <it>An. farauti s.s</it>. expanded much earlier on Malaita (<it>t</it>_exp= 24,600 BP) than the populations on Guadalcanal (<it>t</it>_exp= 16,800 BP for <it>An. farauti s.s</it>. and 14,000 BP for <it>An. irenicus</it>).</p> <p>Conclusion</p> <p>These findings suggest that <it>An. irenicus </it>and <it>An. farauti s.s</it>. are monophyletic sister species living in sympatry, and their populations on Guadalcanal have recently expanded. Consequently, the findings further suggest that <it>An. irenicus </it>diverged from the ancestral <it>An. farauti s.s</it>. on Guadalcanal.</p

Estimation of the sporozoite rate of malaria vectors using the polymerase chain reaction and a mathematical model.

We developed a sensitive polymerase chain reaction (PCR) method for the detection of Plasmodium falciparum DNA from mosquitoes collected in the field. Plasmodium falciparum was detected from 15.2% of 1-parous mosquitoes, Anopheles farauti, in the Solomon Islands through use of the PCR method. A novel mathematical model was developed to estimate the sporozoite rate based on the malaria-positive rate of 1-parous mosquitoes. Using this model, the sporozoite rate of Anopheles farauti in the Solomon Islands was calculated to be 0.09%. This method enables estimation of the sporozoite rate based on a relatively small number (100-200) of mosquitoes compared with the number needed for the ELISA method.</p