Iterative annotation to ease neural network training: Specialized machine learning in medical image analysis

Neural networks promise to bring robust, quantitative analysis to medical fields, but adoption is limited by the technicalities of training these networks. To address this translation gap between medical researchers and neural networks in the field of pathology, we have created an intuitive interface which utilizes the commonly used whole slide image (WSI) viewer, Aperio ImageScope (Leica Biosystems Imaging, Inc.), for the annotation and display of neural network predictions on WSIs. Leveraging this, we propose the use of a human-in-the-loop strategy to reduce the burden of WSI annotation. We track network performance improvements as a function of iteration and quantify the use of this pipeline for the segmentation of renal histologic findings on WSIs. More specifically, we present network performance when applied to segmentation of renal micro compartments, and demonstrate multi-class segmentation in human and mouse renal tissue slides. Finally, to show the adaptability of this technique to other medical imaging fields, we demonstrate its ability to iteratively segment human prostate glands from radiology imaging data.Comment: 15 pages, 7 figures, 2 supplemental figures (on the last page

A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology

Background: Image-based machine learning tools hold great promise for clinical applications in pathology research. However, the ideal end-users of these computational tools (e.g., pathologists and biological scientists) often lack the programming experience required for the setup and use of these tools which often rely on the use of command line interfaces. Methods: We have developed Results: By segmenting glomeruli, interstitial fibrosis and tubular atrophy, and vascular structures from renal and non-renal WSIs, we demonstrate the scalability, best practices for transfer learning, and effects of dataset variability. Finally, we demonstrate an application for animal model research, analyzing glomerular features in three murine models. Conclusions

Iterative annotation to ease neural network training: Specialized machine learning in medical image analysis

Neural networks promise to bring robust, quantitative analysis to medical fields, but adoption is limited by the technicalities of training these networks. To address this translation gap between medical researchers and neural networks in the field of pathology, we have created an intuitive interface which utilizes the commonly used whole slide image (WSI) viewer, Aperio ImageScope (Leica Biosystems Imaging, Inc.), for the annotation and display of neural network predictions on WSIs. Leveraging this, we propose the use of a human-in-the-loop strategy to reduce the burden of WSI annotation. We track network performance improvements as a function of iteration and quantify the use of this pipeline for the segmentation of renal histologic findings on WSIs. More specifically, we present network performance when applied to segmentation of renal micro compartments, and demonstrate multi-class segmentation in human and mouse renal tissue slides. Finally, to show the adaptability of this technique to other medical imaging fields, we demonstrate its ability to iteratively segment human prostate glands from radiology imaging data.Comment: 15 pages, 7 figures, 2 supplemental figures (on the last page

Pharmacies as providers of expanded health services for people who inject drugs: a review of laws, policies, and barriers in six countries

Background: People who inject drugs (PWID) are underserved by health providers but pharmacies may be their most accessible care settings. Methods: Studies in the U.S., Russia, Vietnam, China, Canada and Mexico employed a three-level (macro-, meso-, and micro-) model to assess feasibility of expanded pharmacy services for PWID. Studies employed qualitative and quantitative interviews, review of legal and policy documents, and information on the knowledge, attitudes, and practices of key stakeholders. Results: Studies produced a mixed assessment of feasibility. Provision of information and referrals by pharmacies is permissible in all study sites and sale and safe disposal of needles/syringes by pharmacies is legal in almost all sites, although needle/syringe sales face challenges related to attitudes and practices of pharmacists, police, and other actors. Pharmacy provision of HIV testing, hepatitis vaccination, opioid substitution treatment, provision of naloxone for drug overdose, and abscess treatment, face more serious legal and policy barriers. Discussion: Challenges to expanded services for drug users in pharmacies exist at all three levels, especially the macro-level characterized by legal barriers and persistent stigmatization of PWID. Where deficiencies in laws, policies, and community attitudes block implementation, stakeholders should advocate for needed legal and policy changes and work to address community stigma and resistance. Laws and policies are only as good as their implementation, so attention is also needed to meso- and micro- levels. Policies, attitudes, and practices of police departments and pharmacy chains as well as knowledge, attitudes, and practices of individual PWID, individual pharmacies, and police officers should support rather than undermine positive laws and expanded services. Despite the challenges, pharmacies remain potentially important venues for delivering health services to PWID.Other UBCNon UBCReviewedFacult