NCL-SM: A Fully Annotated Dataset of Images from Human Skeletal Muscle Biopsies

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include $>$ 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Introducing NCL-SM: A Fully Annotated Dataset of Images from Human Skeletal Muscle Biopsies

Single cell analysis of skeletal muscle (SM) tissue is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be precise. There is currently no tool or pipeline that makes automatic and precise segmentation and curation of images of SM tissue cross-sections possible. Biomedical scientists in this field rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to get the segmentation right. We believe that automated, precise, reproducible segmentation is possible by training ML models. However, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human tissue sections from healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include $>$ 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibres and annotated reasons for rejecting low quality myofibres and regions in SM tissue images, making this data completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Shifting Capsule Networks from the Cloud to the Deep Edge

Capsule networks (CapsNets) are an emerging trend in image processing. In contrast to a convolutional neural network, CapsNets are not vulnerable to object deformation, as the relative spatial information of the objects is preserved across the network. However, their complexity is mainly related with the capsule structure and the dynamic routing mechanism, which makes it almost unreasonable to deploy a CapsNet, in its original form, in a resource-constrained device powered by a small microcontroller (MCU). In an era where intelligence is rapidly shifting from the cloud to the edge, this high complexity imposes serious challenges to the adoption of CapsNets at the very edge. To tackle this issue, we present an API for the execution of quantized CapsNets in Cortex-M and RISC-V MCUs. Our software kernels extend the Arm CMSIS-NN and RISC-V PULP-NN, to support capsule operations with 8-bit integers as operands. Along with it, we propose a framework to perform post training quantization of a CapsNet. Results show a reduction in memory footprint of almost 75%, with a maximum accuracy loss of 1%. In terms of throughput, our software kernels for the Arm Cortex-M are, at least, 5.70x faster than a pre-quantized CapsNet running on an NVIDIA GTX 980 Ti graphics card. For RISC-V, the throughout gain increases to 26.28x and 56.91x for a single- and octa-core configuration, respectively.